The first episode of Red vs. Blue introduces the main characters, and poses the all-important question, why are we here?

The Reds get a new piece of equipment, and Grif has a problem with its name.

The Red and Blue armies get new recruits.

Caboose is given the job of "guarding the flag". Donut goes to the store.

Donut returns from the store with a surprise.

The Blues go through the teleporter. The Reds get the upper hand.

While Church and Tucker lament their current situation, Caboose hops into the tank.

Grif and Simmons flee as Caboose's trigger happy firing has dire consequences.

The cavalry arrives, and Caboose gets stuck.

Tucker requests reinforcements, and gets more than he bargained for.

Tex assaults the Red Base, injuring donut and knocking out Grif and Simmons.

Church reveals that Tex was his former girlfriend and the Red Team airlifts a severely injured Donut back to headquarters.

Simmons and Grif guard Tex while Church explains to the Blues about Tex's AI.

The Blues fake an attack on the Reds in order to free Tex and inadvertently get Sarge shot in the head.

Sarge and Church meet up in the spirit world and talk about the afterlife until Sarge is revived by Grif.

Donut returns with new armor, and Lopez finally speaks.

The origin points here.

Church tries to warn the Red Team of Tex's impending attack.

The final episode of Red vs. Blue season one.

Three months after Tex's second attack on the Red Base, Medical Officer DuFresne ("Doc") arrives in Blood Gulch and contacts Blue Command for orders. He reports to the Blue Team to treat Tex, who has already died.[2] Church explains this to Doc, noting how his and Tex's bodies are both buried in front of Blue base. More helpfully, Caboose conveniently recaps the first season, explaining that Church is actually a ghost possessing Lopez's robot body, which has since been spray-painted cobalt. Caboose has also apparently begun to habitually utter death threats to Tucker in a deep, menacing voice. With nobody injured, Doc, on loan to both armies due to a lack of resources, prepares to visit the Red Team next, but the Reds suddenly attack.

With the Reds continuing their attack, Church and Tucker argue over defense strategy. Despite his protest that he is only a medic, DuFresne is officially nicknamed "Doc" by Church, who coerces him into helping by shooting Caboose's pinky toe. Meanwhile, the Reds run out of ammunition, due to Grif's failure to bring extra rounds, and consequently try to bluff the Blues into surrendering.

The two teams negotiate terms. The Reds demand Lopez's return, but Church is loath to surrender his new body; instead, he cedes Doc as a hostage. In return, Grif is forced to publicly humiliate himself, to the delight of all, particularly Sarge.

In order to repair Sheila, Church and Tucker try to determine how to activate the repair sequence in Church's robot body. Church only manages to find the time and temperature function, but Tucker discovers a small switch on Church's crotch. When flipped, it activates a strange beeping noise audible only to Church. Back at the Red Base, the Warthog begins to beep, and announces that its homing beacon has been activated.

Sarge reveals that he had put a remote control in the Warthog to allow Lopez to drive it remotely. Meanwhile, Church, who cannot stand the remote's beeping sound, begs Tucker and Caboose to deactivate it, but the switch breaks. While the other Blues continue trying to help, Church unwittingly causes the Warthog to scoop up Doc and then to attempt to kill Sarge. Having pinned the latter against the wall of Red Base, the Warthog slowly advances its firing machine gun toward his head as the episode ends.

Tucker disconnects the wire that had connected to Church's switch, thereby stopping the beeping noise, but also disabling Church's legs. The Warthog deactivates, sparing Sarge. Driving the Warthog, Doc attempts to unpin Sarge, but only manages to ram him into the wall twice more, and the Reds consequently decide to return him to the Blues. When Simmons and Grif arrive at the Blue Base, they see Tucker still kneeling in front of Church attempting to repair his legs, and quickly jump to conclusions.

The Blues refuse to accept Doc back from the Reds, fearing that he might be spying for them. The Reds eventually give up and return to their base. Doc attempts to return with them, but the Reds quickly ditch him, leaving him alone. Doc attempts to return once more to the Blues, but they remain suspicious of him and reject him again.

At the Red Base, Donut unsuccessfully attempts to engage Sarge in idle chatter while waiting for Simmons and Grif to return. The two eventually do arrive back and report their failure. Back at the Blue Base, with Church still immobile, Caboose suggests that Church leave his body, so that Lopez can make any repairs to himself and Sheila. After expressing surprise that such a clever idea had come from Caboose, Church and Tucker endorse the plan. Church leaves Lopez's body, but Tucker and Caboose pay no attention to Lopez, who flees before Church can reappear in spirit form. The Blues then chase after him. Meanwhile, the Reds spot Lopez running toward their base, and mistake him for a Blue. Sarge and Simmons prepare to counterattack, while Donut annoys Grif with more idle chatter.

Tucker and Caboose catch up to Lopez, who refuses to re-join them and instead orates at length about oppression and the advent of a new day for his people. Sarge and Simmons try to run him over with the Warthog having mistaken him for a Blue soldier, but Lopez activates the Warthog's remote destruction sequence in self-defense and, feeling betrayed, defects to the Blues.

*

Released on April Fool's Day and the anniversary of Red vs. Blue's first episode, the episode begins with Grif and Donut crying over the graves of Sarge and Simmons, following the events of episode 28. Sarge appears and explains that he had only been napping, and had escaped by eating his way out of the ground with his spoon. Simmons' ghost appears to give the Red team a warning, but Donut shoots and kills him, explaining that Simmons' ghost is actually "Ol' Man Caboose". Tucker and Doc appear and announce their engagement, over which a French-speaking Lopez, apparently in love with Tucker, laments. Church awakes and realizes that this episode had apparently been merely a dream, when he finds himself confronted by the French-speaking Lopez.

The Blues convince Lopez to repair Sheila. As he works, Grif spies him through a sniper rifle and assumes that there is a "new" Blue soldier. The Red Team discusses various explanations. Donut manages to guess the truth, but no one believes him. Once Lopez finishes repairs, he and Sheila fall in love with each other, much to Caboose's dismay. To disrupt the odd love triangle, Church attempts to possess Lopez again, but is unsuccessful; instead, it is Tex who suddenly appears in Lopez's body.

While Caboose talks to a now-confused Sheila, Tex reveals to the rest of the Blues that she had been watching them for some time and had noticed Caboose's aggressive behavior. She explains that her former artificial intelligence (AI), O'Malley, had jumped via radio to Caboose when it had assessed that she was unlikely to survive her second attack on the Red Base at the end of season 1. Using Lopez's body as a bargaining chip, she asks Church's help in killing the AI. Meanwhile, at the Red Base, Sarge realizes that the Reds no longer have anyone with an ability to repair things and, after some arguments, prepares to turn Simmons into a cyborg.

Tex explains that everyone in Blood Gulch must turn off their radios so that O'Malley will be unable to jump into someone else's armor when flushed out of Caboose. The ghosts of Church and Tex jump into Caboose's mind to find O'Malley. They meet Caboose's mental image of Tucker, as well as Caboose's inner self. The real Tucker and Lopez take Sheila to the Red Base to convince the Reds to turn off their radios.

In Caboose's mind, Tex and Church meet Caboose's mental image of the latter — vulgar, insulting, and under the impression that he is "Caboose's best friend". At the Red Base, Donut and Grif search near the Warthog for a part needed for Simmons' cyborg operation and begin to panic when they see Sheila, Tucker, and Lopez approaching. The episode ends with Tucker having difficulty in trying to brake Sheila.

Donut flees from the approaching Blues, but, still unable to brake, Tucker runs over Grif and the Warthog with Sheila. Tucker radios the Red Team to tell them to turn off their radios. Initially they refuse, so Lopez sings a love song about Sheila over the radio until they relent. Meanwhile, Church and Tex meet Caboose's mostly incorrect mental images of the Red Team. O'Malley suddenly kills Caboose's mental image of Church — thus making Caboose completely forget who Church is — and the real one and Tex subsequently give chase. Eventually trapping O'Malley, the two, hoping that Tucker had been successful, shoot him, chasing him out of Caboose's mind. Without any means of jumping to another armor, O'Malley signals "cockbites" in Morse code as he gradually fades. However, in a scene deleted from the DVD he detects one last radio transmission from Doc, who is attempting to contact Blue Command, and takes possession of him.

Disoriented from the events of the previous episode, Doc discovers a hovercraft in a cave and consults with Vic, who proves to be unhelpful. Meanwhile, Tex has disappeared, and Grif awakes from surgery to find that Sarge has replaced most of his organs, which had been damaged in the accident with Sheila, with those left over from Simmons' cyborg operation.

With O'Malley having previously killed Caboose's mental image of Church in episode 33, Church unsuccessfully tries to re-establish Caboose's memory of him. At the Red Base, Simmons chides Grif for continuing his old unhealthy habits in his rebuilt body. Sarge announces the need to re-acquire Lopez, as his memory contains secret plans from Red Command.

Caboose is jealous of the relationship between Lopez and Sheila, who are now refusing to work due to perceived poor treatment by the soldiers — that is, being repeatedly blown up, possessed or left outside to rust. Eventually, they consider forming their own robot army. At the Red Base, Sarge sends Grif and Donut out to try to spy on the Blue Team. While on the mission, Grif, who cannot stand Donut's childish behavior, tricks him into exploring the caves by himself. Donut then spots Doc and O'Malley talking to each other, in the manner of Gollum and Sméagol in The Lord of the Rings. Overhearing O'Malley's evil plans, Donut tries to return to his base, only to become lost and eventually captured at the Blue Base.

As a note, "Nut. Doonut." — a reference to James Bond's introduction, "Bond. James Bond." and use of two 0's in his agent number, 007 — is the episode title as listed on the Rooster Teeth website and on the Red vs. Blue: Season Two DVD. However, the six versions downloadable from the Internet show different titles, each another reference to the James Bond series (specifically, the six starring Sean Connery): "Blunderball" - Thunderball, "Dr. No-No" - Dr. No, "You Only Spawn Twice" - You Only Live Twice, "From Blood Gulch With Love" - From Russia with Love, "Dummies Are Forever" - Diamonds Are Forever, and "Pinkfinger" - Goldfinger.

The Blues attempt to interrogate Donut, without much success. Church then possesses Donut and, using him as a hostage and a puppet, negotiates with the Reds to have them to build new robot bodies for himself and Tex. While Tucker continues to haggle with Sarge over the specifications for the robots, Church leaves Donut's body and returns to Blue Base to find that Lopez and Sheila are missing.

Church discovers a note from Sheila and Lopez confirming that they have started a robot army. At the Red Base, Sarge unveils the two new robots; one contains a microphone to spy on the Blues, and the other contains a bomb. The Reds and the Blues meet in the center of the gulch to execute the exchange. Sheila and Lopez also arrive to conquer the Blues; Lopez becomes angry at seeing new robots brought into the conflict, and rushes forward to attack. A tense Mexican standoff results, and Sarge tries to call an air strike. However, due to crossed communication channels, Tucker intercepts his message, and realizes that Vic is apparently working for both Red and Blue Commands. While Church possesses one of the robots, Tucker tries to alert everyone that Red and Blue are the same, but is hit by a rocket before anyone can understand him. His attacker is apparently Doc, possessed by O'Malley, who flies around on the hovercraft, firing rockets at will. In the ensuing chaos, O'Malley takes Lopez as a hostage, announces his intention to conquer the universe, and disappears through the Red Team's teleporter. The Reds and Blues call a temporary truce to pursue Doc, whom the Blues need to heal Tucker, and to retrieve Lopez, whom the Reds need for the plans his memory contains. Donut, Sheila, Tucker, and one of the robots remain behind in the gulch while everyone else follows through the teleporter. Tex soon surfaces in the remaining robot body. Unfortunately, due to a teleporter malfunction, the pursuing Reds and Blues end up separated and scattered across different places. Simmons ends up in a huge area full of teleporters, Church and Grif end up captured by Max Gain, a member of the Red team in Sidewinder, and Sarge and Caboose appear in the stream in Battle Creek.

Donut tries to coax an injured Tucker into getting up, conveniently providing a recap of the end of the previous season in the process. Sarge and Caboose find themselves in Battle Creek, in the midst of perpetually respawning Red and Blue soldiers ("Grunts"), who engage in a complex action sequence that lampoons multiplayer game sessions in Halo. Meanwhile, Simmons is lost in a place full of teleporters (the Chiron TL34 map), and Grif and Church have been imprisoned by the Red Team on Sidewinder.

In an unknown location, Wyoming, another freelancer, interrogates a soldier named Phil, but is interrupted by a phone call hiring him for another job. Meanwhile, still in Battle Creek, Sarge and Caboose steal the Red and Blue flags in an attempt to coerce the teams to help them find their way out. When that fails, Caboose recalls O'Malley's possession, unleashes his angry side, and single-handedly eliminates both teams. Simmons then retrieves them via a teleporter.

O'Malley calls Vic and reveals his plot to eliminate both the Red and Blue Teams and to rule the universe. He also informs Vic that, to preserve Vic's secret, he has hired an assassin to kill Tucker, the only person who knows that Blue Command and Red Command are the same. Back in Blood Gulch, Tex tells Tucker that Wyoming, the assassin hired to kill him, is a freelancer from the same experimental program as Tex, and, like Tex, he had been enhanced with artificial intelligence. Still in the teleporter hub with Simmons and Caboose, Sarge contacts Donut to inform him of the "Blue plot" and that Tucker's idea that Red and Blue are the same is nothing but a deception. Wanting to help to find Church, Caboose unwittingly presses a button that activates the bomb in Church's robot body. On Sidewinder, Church consequently lets out a large belch, and his stomach begins to tick.

Simmons reprograms a teleporter and advises Donut on how to reprogram the Reds' teleporter in Blood Gulch. On Sidewinder, Wyoming kills all of the Reds and tells Church and Grif that he is leaving them to starve to death. Meanwhile, everyone else emerges from the teleporter on Sidewinder, Tucker covered with "black stuff" (which luckily prevents Wyoming from recognizing and shooting him). While Donut and Caboose clean off Tucker's armor, the jail cell holding Church and Grif mysteriously opens. Wyoming spots Tucker from afar and aims at him; Tex ambushes him, but O'Malley, Wyoming's employer, ambushes her.

O'Malley activates Lopez's "secret weapon", a weather control device that Sarge had almost finished. The Red and Blue Teams join forces to confront O'Malley, who begins to wreak havoc with his rocket launcher. Simmons manages to teleport the Battle Creek players to Sidewinder and convinces them to attack and defeat O'Malley. Lightning from Lopez's weather device hits Church, thereby damaging the bomb in his body. When Sarge is subsequently unable to disable the bomb, Tucker tries to destroy Church with O'Malley's rocket launcher before Church explodes, but Wyoming snipes the launcher out of Tucker's hand. The bomb explodes and, due to the damage received from the lightning, destroys the present as well, sending both teams (except Church) to the future (Halo 2). Donut attempts to direct a play to explain this sequence of events to Tucker. The group reasons that they were blown into the future because they were standing in front of Church; Tucker deduces that Church must have been blown into the past. Meanwhile, on a Marathon 2 map, Church appears, wondering what has happened.

Exploring the wasteland in the future, Grif, Simmons, and Tucker discuss various Hollywood post-apocalyptic clichés. The group finds a jeep and bickers over it. Tucker is bent on finding Church, but Sarge asserts that Church, along with the group's enemies, had died in the explosion. Meanwhile, a cackling O'Malley discovers Lopez's disembodied head on a beach.

While Sarge and Donut try to repair the Warthog, Grif, Tucker, and Simmons argue about styling the jeep in order to attract women. Tucker still maintains that Red and Blue are the same, but no one believes him. Meanwhile, O'Malley, Doc, and Lopez inspect some real estate (Zanzibar in Halo 2); O'Malley and Doc argue over its viability and over how the computer inside should be used. This episode marks the final appearance of the weapon reticle in footage filmed with Halo 2; going forward, the Rooster Teeth team has exploited a gameplay bug to remove it.

(Episode 45.9) Available only to sponsors or on the Season 3 DVD and produced solely by Gustavo Sorola while the rest of the production crew had been out of town. This episode continues or replaces the events of episode 45, though is non-canon, and features paper cutouts as characters while portraying Simmons as a hero.

Having moved into the fortress, O'Malley, Doc, and Lopez repair the turret emplacements and meet The Red Zealot, who believes that he has found a holy temple. Exploiting the Red Zealot's religious fervor, O'Malley deceives him into performing menial tasks for him. O'Malley then catches a glimpse of Tex, who is spying on him, but on subsequent glances, sees nothing. Elsewhere, Sarge, Grif, and Simmons discuss the results of Grif and Simmons' failed reconnaissance, and, while attempting to push the Warthog out of a ditch, receive a transmission from Tex informing them of O'Malley's location.

The Reds, Tucker, and Caboose meet with Tex on the beach near O'Malley's fortress, where she reveals her plan to destroy both O'Malley and the entire base by planting a bomb inside. Tex has scouted the base and found the exact location to place the bomb. However, citing the bomb's immense weight, she has someone else carry it; of the others, only Caboose can lift it. Meanwhile, the Red Zealot informs O'Malley and Lopez that a crowd of people is gathering on the beach. Upon learning that Lopez is inside with O'Malley, the Reds balk at destroying the base, but Tex refuses to risk losing her chance to defeat O'Malley. Tucker solves the problem by reminding the Reds that, since Tex is a mercenary, they can simply hire her to help them to retrieve Lopez. Tex agrees to this arrangement for a future favor.

After discarding two of Sarge's suicidal battle plans, the Blood Gulch group invades O'Malley's fortress and are pinned down by mini-gun turrets manned by the Red Zealot and Lopez's head. Tex snipes Lopez's head off his turret, but the Zealot pins her down with gunfire. Simmons and Grif manage to enter the base and move on to look for O'Malley. Tucker, who had fallen into a hole near the windmill, finds a mysterious sword, and uses it to kill the Red Zealot. Meanwhile, carrying the bomb inside the fortress, Caboose mistakes Tex's "X" marking for a plus sign. He continues on and stumbles across a computer, from which he hears the voice of Church.

In the past, Church (as a Marathon character) finds a computer terminal, which answers some questions for him. Church is in the housing facility for The Great Weapon, which The Great Destroyer will use to bring Great Doom to the galaxy in 1,856 years. When computer describes The Great Destroyer as a "blue being" who "will be known as the stupidest life form in the universe", Church assumes that it must be referring to Caboose. 1,856 years in the future, Caboose asks Sarge to look at the computer terminal, which is playing a message from Church. The message tells Caboose not to touch anything, lest he bring about Great Doom. Specifically, Caboose should avoid bringing the "glowing sword weapon thingy" into the base, as the place will lock its doors. Tucker and Donut stroll in with the sword, and the base locks down, with Caboose's bomb already counting down inside it. In the past, Church finishes recording his message, but, deciding that it will not suffice, asks the terminal to transport him to Blood Gulch so that he can prevent the whole fiasco. While telling jokes to pass the time, the terminal begins the millennium-long process of researching and building a teleporter.

The computer completes the teleporter and reveals its name to be Gary. Church teleports back to Blood Gulch shortly before the series begins. The moment Church is teleported away, however, another Church runs in and tells Gary to teleport him to Sidewinder instead, because he screwed everything up.

Back at Blood Gulch prior to the events of episode 1, this Future Church decides to try and prevent the death of Tex, which would prevent O'Malley from escaping and causing the events leading up to The Great Doom. He finds, however, that he either has no effect, or causes the events by his presence in the first place:

* Lopez's legs malfunction because Future Church, in trying to get him a larger switch, kicked dirt into the switch Sarge decided to use when building the robot.

* Prior to episode 1, the Blues were under the charge of Captain Butch Flowers. Knowing Flowers would die, Future Church gives him aspirin, but Flowers dies of a heart attack due to an allergy of the medicine. Tucker, at this point in Blue armor, takes Flowers' cyan armor.

* Donut, in rookie Red armor, finds the Blue Base and steals the flag because Future Church, failing to recognize him outside of pink armor, gives him directions.

* Future Church attempts to prevent the death of his past self, which would stop Tex from arriving in Blood Gulch. He awakens the tank and runs through her protocols to try and prevent her from shooting him later. She refers to herself as Phyllis, and overrides her name when Church addresses her as Sheila. Future Church turns off a "friendly fire protocol," which in actuality prevents friendly fire; thus the original Church's death takes place because of Future Church.

* Finding a sniper rifle on the corpse of his past self, Future Church picks it up but drops it later. Caboose finds it, and uses it to shoot Sarge.

* Attempting to kill Donut to stop him from killing Tex, Future Church fails and retreats to the cave, frustrated. Caboose spots what "looks like Church," and turns on his radio. As a result, O'Malley infects him.

The funeral of Church and Tex, prior to the events of Season 2, takes place. Future Church continues his attempts to change things for the better, but still ends up causing the disasters he was trying to prevent:

* Future Church, posing as Captain Flowers, contacts Vic to try and get him to tell the Reds to get rid of Doc, to stop the medic from being infected by O'Malley. Vic misconstrues his words to believe the Red and Blue teams have merged, but that the soldiers must not know. Thus, the Red and Blue Commands merge.

* To stop them from making a robot army, Future Church tries to dissuade Lopez and Sheila from the idea. Instead, he gives them the idea himself, and they decide to build and hide a rocket-launching vehicle in the caves.

* Future Church decides to fix the Red teleporter before it malfunctions and sends the characters to various places, just as Sheila rams the base. Future Church is knocked out, and the teleporter begins giving off sparks.

* During the Mexican standoff where O'Malley appears, Future Church finds a rocket launcher and aims to take the villain out. Instead, he shoots and injures Tucker from behind, and again decides to retreat to the caves.

Future Church watches Tex, Donut and Tucker leave for Sidewinder, and soon follows them. He talks first to Sheila before leaving for Sidewinder, asking her to do him an inaudible favor. Once at Sidewinder, Future Church finds his past self and Grif in prison, and opens their cell by pressing a button in another room. He attempts to contact Tex, who is currently being held by O'Malley and Wyoming, before another Church approaches him. This new Church claims that he fails to stop the bomb, and gets blown back in time again, only to return to Sidewinder. He then tells Future Church to "meet us at the top of the ramp."

The bomb goes off, and Future Church is sent back in time. As seen in Episode 50, as soon as Church is teleported by Gary to Blood Gulch, Future Church arrives and asks to be sent to Sidewinder because he screwed everything up. Just then, more Churches arrive, each having been unsuccessful to stop the bomb, and thus sent back in time to Gary. These Churches all meet in Sidewinder, and explain to the newest Church how their various plans failed. It is determined that whichever Church did each one of these plans already must be the successful Church, since he isn't sent back in time again. This Church gives up on trying to correct everything, instead freeing Tex, and rejoining the Blood Gulch soldiers before the explosion, thus being sent into the future.

Church emerges at O'Malley's base, just in time to ask Gary, who remains there, to stop the bomb from detonating. He then prepares to explain the events he went through.

Caboose asks Church why he did not try to save himself, Tex, or create millions of copies of himself trying to defuse the bomb when he was in the past. Church warns Tucker that Gary said the sword was dangerous, but Tucker blows it off. Meanwhile, the Reds covertly meet to discuss a distress signal on the Red Army's open channel, which was picked by the radio in the Warthog. This episode features an unknown character ducking behind a rock.

The Blues watch the Reds play with their radio, at a loss for a motive. Caboose explains that they are talking about the distress signal, an explanation he got from "Andy". The Reds are discussing the distress signal, which Simmons cannot pinpoint due to the substandard equipment. Caboose introduces Tucker and Tex to "Andy": the deactivated bomb. Predictably, it won't talk to them. However, Gary the terminal knows Andy very well. This episode also features another distant character.

Andy starts talking to the rest of the Blue Team, and is quickly revealed to be rude and volatile. Caboose and the Blues try to calm him down so he won't explode. Meanwhile, the Reds are planning on escaping in the Warthog to find the source of the distress signal. Grif is sent to find out what the Blues are doing, only to be confused when he finds them trying to soothe Andy. Unbeknownst to all, O'Malley has assembled a huge army of robot Lopez duplicates outside the base, which he orders to kill everyone and retrieve the "device".

The Reds puzzle over why the Blues were talking to the bomb, and Sarge concludes that they are trying to re-arm it as part of a pre-emptive attack strategy. O'Malley's army turns out to be extremely slow-moving: Lopez built them that way so they would win in exactly 24 hours, since O'Malley said he wanted a day of victory. Meanwhile, the Blues have finally managed to calm Andy down, but are interrupted by explosions and plasma fire as O'Malley's attack begins. Believing that the Blues are attacking, Sarge orders the Reds into battle.

O'Malley berates Lopez for creating such a slow moving army. In revenge, Lopez tricks O'Malley into insulting himself in Spanish. The Reds flee the battle in the Warthog to track down the distress signal. Donut is left behind to discourage pursuit, but manages to steal O'Malley's hovercraft and rejoin his teammates. Tex steals Tucker's sword so she can fight the robots; Church decides that she must be The Great Destroyer from the prophecy. An unseen figure wipes out O'Malley's army with a volley of plasma grenades, and then attacks a startled O'Malley. Lopez's fate is left unrevealed.

Shortly after Donut catches up with the other Reds in a cave, Simmons and Grif track the signal out of the cave, finding themselves back in Blood Gulch (Coagulation in Halo 2). This discovery is accompanied by a lengthy scream of "Noooooooooo!" from Grif. Back at the fortress again, Church and Tucker admire the slaughtered robots and congratulate Tex, but she admits she's not responsible: she was in the basement, trying to get the sword to work. Church rushes over to Gary to question him about the identity of The Great Destroyer, unaware that an Alien is sneaking up on him.

Grif is still despairing over being back in Blood Gulch, despite the others' attempts to shut him up. Meanwhile, back at Zanzibar, Tex, Tucker, and Caboose discover that Church is back in ghost form again. Church explains that he was literally scared out of his body after being ambushed by the Alien in the last episode, though his attempts to explain this are repeatedly interrupted by Caboose's stupidity and Tucker's attempt to hijack the flashback and showcase his sexual fantasies; Tucker wisely ends quickly so as to avoid getting his head blown off by Tex. Tucker uses the catch phrase "Bow-chicka-bow-wow" in this episode for the first time, much to Church's annoyance.

In Blood Gulch, the Red Team takes potshots at Grif with their sniper rifles in order to get him to stop screaming. Grif eventually relents, and the team prepares to investigate their old base. Sarge gives a speech about alertness, completely unaware that Sheila is roaming around behind him. Meanwhile, the Blues prepare to hunt the Alien that scared Church. When asked about the Alien's whereabouts, Andy proves unhelpful, merely offering insults instead. Suddenly, the Blues spot the Alien, causing them to fire wildly and run away in panic - with the exception of Caboose, who simply asks, "Did we win?". The episode ends with Andy laughing and mocking the sudden retreat.

Simmons tries to convince Sarge that he did see a tank behind him. Donut concurs, but Sarge disregards his testimony because he is "impressionable", and Grif simply denies it in order to make Simmons look bad. Meanwhile, the Blues insult each other over their previous panicked, wild fire attack on the alien. Tex decides to go in alone and dashes into the complex while the rest debate Church's heroism (or lack thereof). Upon entering the complex, Tex is immediately cut down and re-appears in ghost form. Back at Blood Gulch, Simmons and Donut get into a fistfight/hijacking match over the hovercraft, which Simmons wants to use to find the tank. Believing that Simmons has gone insane, Sarge promotes Grif to his "Number Two" man, but Grif quickly loses the position due to his laziness. On the Blue side, Tucker suggests that Caboose goes into the complex and speak to the alien. Church likes the idea because he and Tex could sneak in and retrieve their bodies while the Alien is chewing on Caboose. Caboose enters, sees Andy, and asks whether he has seen the Alien. As he finishes his sentence he sees the Alien's shadow on the ground.

Simmons has completely fallen out of favor with Sarge, and in fact is now ordered by the judge — Donut wearing a judge's wig — to stand at least 200 yards away from the rest of the Reds. As a result, Sarge begins to hold a competition to determine who will be his new right-hand man. Grif is automatically disqualified for being Grif, which puts the competition down to Donut, Lopez's old wrench, and a skull found nearby. Simmons laments the ruination of his life, and concedes to himself that maybe he did imagine seeing the tank. Sheila's voice is suddenly heard right behind him, begging to differ. Meanwhile, back at Zanzibar, the Blues are startled to discover that Caboose has actually managed to tame the Alien, thanks to his kindness — or, more likely, that the alien found him unpalatable, and no longer wants to eat him or anything that looks like him. The Blues insult the alien while trying to understand its language, which seems to consist entirely of blarg and honk.

At the Zanzibar fortress, Church asks Gary whether he can translate the Alien's speech for them. Gary reveals the alien's race were his creators, but unfortunately he knows virtually nothing about the race because he was programmed entirely with knowledge of the Shisno. The Blues continue to try translating what the alien is saying, and eventually reach the conclusion that the Alien's name might be "Honk Honk". Church even believes that he figured out that blarg means yes in the alien's language, though Tex argues that it could also mean no. Meanwhile at Blood Gulch, the Reds continue Sarge's right-hand-man contest, which Donut ultimately wins. Simmons has become despondent and suicidal, and Sheila (whom Simmons believes is a figment of his imagination) tries to cheer him up by leading him back to her home, a reconstructed Blue base. Sheila reveals that she has lost many of her memories due to circuit degradation over the years. She knows that her final mission was to protect the Blue Base from the enemy of the Blues, and though she has forgotten their identity, she vaguely remembers it was an army of a different color. Simmons, immediately realizing that his life is in danger, unsuccessfully tries to convince Sheila that the enemy was space pirate cowboy monkey ninjas who were trying to round up some cattle.

The episode opens up again at the Zanzibar fortress as Tucker and Caboose are attempting to teach English to the Alien. Church and Tucker get into a small debate on whether they should teach the alien English or learn his language. Tucker is convinced that they should teach English to the Alien and even had created some visual aids. As it turns out, Tucker was able to get the writing supplies from Caboose's gun which apparently contained crayons instead of bullets. However, when Tucker activates his energy sword to cut the poster boards, the Alien jumps over and attacks him. Despite Tucker's cries for help, Church watches the Alien as it attacks Tucker in order to "evaluate" his fighting style.

Back at Blood Gulch, Simmons is at the Blue base with Sheila close by. He attempts to contact the Red Base, but is greeted with Donut on the line, who tries to impersonate an answering machine. Simmons attempts to get Sarge on the line, but Donut, under instructions from an off-screen Sarge, denies Simmons from communicating with Sarge, even after he informed Donut that he had captured the Blue Base and Sheila. Eventually Donut hangs up on Simmons, but not before letting Simmons know that he really enjoys his new job as Sarge's right-hand man. Simmons then declares that he will kill all the Reds and tells Sheila to "lock and load".

Back at Zanzibar, Tex talks with Andy. Tex, through some bluffing and mild threats of blowing up Andy with a remote detonator, convinces him to help her translate what the alien is saying. This, however, doesn't stop Andy from making rude jokes about Tex acting more male than female.

At Zanzibar, Tex and Church argue over whether to let Andy translate what the Alien is saying. Church is concerned that Andy's lack of manners could upset the alien even further. Eventually, Church relents and agrees to this arrangement out of his curiosity as to what could happen. During this whole conversation the Alien is still beating Tucker to a pulp.

At Blood Gulch, the Reds are fracturing even more as Donut is unsuccessful in asking Grif to return to their base. Grif refuses, believing Sarge simply wants him to do work, and not just eat ice cream. In reality, Sarge did want Grif to help him eat some of the ice cream that he found. Simmons — now painted mostly blue — plays out his vengeance on the Reds. At first he attempts to cause the Reds to be jealous of him; he soon gives up and orders Sheila to attack the Red base.

At Zanzibar, with Andy acting as a translator, the Alien reveals that he came to retrieve the energy sword that Tucker found. It was part of the sacred quest that he was on, but the sword has now locked itself to Tucker as he was the first to find and use it; this explains why Tex was unable to use the sword. As a result, Tucker must join the Alien on its quest. If Tucker refuses, the alien will destroy the base and slaughter everyone in it.

On Zanzibar's beach, Tucker finds himself as an involuntary sword-bearer as he is forced to partake of the sacred quest that has some resemblance to The Lord of the Rings. After the Alien explains the lands that he and Tucker will travel through, Church informs Tucker (the fighter) that Caboose (the wizard), Andy (the archer), and the alien (the healer) will be the team that goes out on this quest. Though this quest is pretty much a suicide mission, Tucker does warn Church that he better hope that Tucker survives, or he will be forced to take care of any children that Tucker might have.

At Blood Gulch, Simmons' attack on the Red Base continues. However, he has been so indoctrinated with hatred of the Blues that all of his insults and attack orders confuse the words Red and Blue. Grif, still watching Simmons and Sheila fire upon the Red Base, convinces Simmons to come back to the Red Base. Despite the selfishness of Grif's reasons, Simmons admits he misses the old days. However, just as he is about to go back to the Reds, Sarge sees that Simmons has painted his armor mostly blue and is unable to accept him back. Sarge says he can understand many things, even the reasons for attacking one's own base out of anger, but to see one of his former soldiers wear the colors of the Blues, is unacceptable.

On the beach of Zanzibar, Church tries to give some last-minute advice and parting words to Tucker and the rest of the quest-team before they begin their trip. Tex apparently has a strong attraction to masculine objects, whether it was Tucker's energy sword, or the Alien's rather muscular naked body, or specifically one part of it. Church attempts to say some encouraging words to Tucker, but this fails as Tucker frustrates Church's attempts. As the team leaves, Church remarks to Tex that he is surprised that she did not go with the rest of the group as quests usually have a goal of riches or power at the end of them. As he finishes his sentence, he assumes correctly that Tex has left.

Back at Blood Gulch, Simmons decides to take Grif back to the blue base as a hostage. After some prodding from Grif about not being "properly treated" as a hostage — in other words, Simmons wasn't being mean to him — Simmons starts hitting him. Simmons pushes Grif into what he thought was a hole, but it turns out to be part of a gravity lift that keeps putting Grif behind Simmons. The episode ends with Simmons getting frustrated each time he pushes Grif into the hole.

Having arrived at the Great Burning Plains (Burial Mounds), the Sacred Quest team prepares to perform one of the many tasks that the hero of the Alien's prophecy is supposed to do. As the team argues and bickers, it is revealed by the Alien and Andy that they know what Earth is, and that they don't have a favorable opinion about the planet. Apparently, the Alien's race invented the telephone a thousand years before humans did, which, however, fails to impress Tucker, due to the limited verbal communication of the alien race. In the meantime, Caboose scouts ahead and claims to recognize the area.

The Alien warns the group that they are about to encounter a monster, which they have to conquer by distracting it and hitting it's weak spot. Tucker is unmotivated about the plan, even to the extent of having paid no attention to the details of the monster's weak spot. After they finally leap down the last ridge, they see the skull of the monster, which Tucker realizes is that of a cow, with a broken skull as the only visible remains, possibly due to one of the Red and Blue Teams' scavenging missions in season 3 (episodes 43–46); Caboose confirms to Andy and the Alien that they had been there before.

Back at Blood Gulch, Sarge assumes that Grif is being tortured by Simmons, a concept he's very satisfied with. Donut, however, in his current status as manager, breaks the harmony by proposing bureaucratic changes. Sarge decides that he can't take this anymore, but is reluctant to rescue Grif - a situation he just can't find the name for, but finally settles with conundrum.

Sarge and Donut enter the Blue Base to rescue Grif without encountering any perimeter defense, such as Sheila. Inside the base, Grif is still playing with the gravity lift that Simmons originally mistook for a hole. As Grif runs to and fro on it, both Simmons and he question how Sheila was able to upgrade the base without any tools or arms. Simmons then concludes that if he could somehow determine the real truth, he could reconcile with Sarge. At this point, Sarge intervenes, knocking Grif out. Before Sarge can execute Simmons for treason, however, Church appears and knocks Sarge out from behind. Church mistakes the mostly blue Simmons as a Blue soldier native to the future.

The Sacred Quest team finds itself in a swamp (Backwash), where Andy says they can rest and sleep for a while. However, with strong allusions to The Lord of the Rings, Caboose notices that something has been following them. Andy confirms that this Gollum-like creature has been following them since the beginning of their journey. Later that night, Tucker awakes to find that he is apparently alone in the swamp. As he begins to look for his companions, the mysterious figure approaches Tucker from behind (as he is being used as bait). The Alien ambushes the intruder, who turns out to be Tex. She then joins the team after being promised the sword upon completion of the quest.

In the basement of the Blue Base in Blood Gulch, Simmons covertly talks to Donut about keeping his true identity hidden from Church. Donut, however, does not actually recognize Simmons. Church soon appears after dropping Sarge's body into the basement, and the three proceed to load Sarge and Grif into the jeep.

Meanwhile, the Sacred Quest team reaches the edge of the Great Freezing Plains (Containment) that the Alien had mentioned. This particular part of the quest requires that the hero gain access to the temple ahead, which is heavily guarded by a large number of guards. With this information, Tucker wants to retrace their steps to recover a mitten that Caboose lost, but Tex takes the initiative and decides to attack the temple guards under the protection of her cloaking device.

Back at Blood Gulch, Church and Simmons drop off Donut and the still-unconscious Sarge and Grif outside the Red Base. Church suggests to Donut that he lie to Sarge and Grif when they wake up, making them think he rescued them. Donut asks what Church wants, based on the precedent set by the Blues' surrender in 22. Church, considering the Reds' failed rescue mission not so much a surrender as a "total ass-kicking", decides to keep the Reds' jeep, causing Donut much despair. As Sarge begins to recover, the episode ends with Simmons knocking him out again in order to protect the secrecy of his identity.

Back at the Freezing Plains, Tex attempts her covert attack inside the temple guarded by the Red and Blue Grunts who first appeared at Battle Creek. Sneaking up behind a blue Grunt, she attempts to knock him out, without much success. Although she has to spend time beating and shooting him, the others pay no attention to his exclamations of pain and complaint. It is only when Tucker yells in reaction to their aloofness that they begin to fire. Now under attack, the rest of Sacred Quest team runs for cover while Tex kills the remaining soldiers in the temple.

In Blood Gulch, Donut, apparently having taken Church's advice to lie and portray himself as a hero, is finishing his debriefing with Sarge and Grif. While the Reds discuss and mock Donut's contrived story, Church briefs Simmons on each Red Team soldier, finishing with a critical opinion of Simmons. His ego thus wounded, the latter runs back to Blue Base to cry. Once out of Simmons' earshot, Sheila asks Church whether he realizes that he had been talking to Simmons. Church confirms that he does.

In Blood Gulch, Church relishes the fact that the Blue Team now possesses all three vehicles within the canyon. Sheila, however, is unhappy and begins to show signs of jealousy and annoyance — this portion was moved to the Deleted Scenes section of the DVD.

Back at the Freezing Plains, Andy frantically orders Tucker to open gates of the temple by using his sword as the key. The doors open, revealing an alien ship. The Alien rushes towards the ship, dropping Andy in the snow. Tex and Tucker become agitated, as the Alien had never disclosed — not even to Andy — that the quest would involve a ship, which Tex demands as her reward, nor that the sword would be used as a key. After taking off in the ship, the Alien appears to make dive attack on the other Quest members; at the last moment it is shown he was firing at a Grunt sneaking up on them. However, the Alien's ultimate intentions are left ambiguous, as Wyoming suddenly guns the ship down. As Tex leaves to pursue Wyoming for destroying her reward (the events of which are portrayed in the miniseries Red vs. Blue: Out of Mind), the Battle Creek soldiers begin to respawn, convincing Tucker and Caboose to leave.

Back in Blood Gulch, Church orders Simmons to wash the Reds' jeep, the latter, unaware that his identity is known, challenges Church's authority. In response, Church tries to demonstrate that he had led the Blood Gulch Blue Team 800 years in the past and, in the process, unexpectedly makes contact with a descendant of Vic. This descendant, who calls himself Vic Jr., scoffs at the idea of "Blue Command", leaving Church confused and wondering the outcome of the Red and Blue civil war.

In the Red Base, Sarge attempts to bury his disgust and hatred toward Grif in an attempt to consolidate whatever soldiers the Reds have left to fight the war with the Blues. Sarge's own personal disdain for Grif still leaks through as he disclosed that he has attempted to murder Grif countless times while everyone was asleep. Outside of the base, Simmons — still mostly blue — and Donut have a verbal fight. Donut, still under the impression that Simmons is a Blue soldier, refused to allow Simmons to pass without being shot at. Eventually, Sarge and Grif come out to see what's happening and acknolwedge who Simmons really is. Simmons, though still looked down upon by Sarge for his apparent betrayal, still wants to pass along Blue Army info to the Reds.

Caboose, Tucker and Andy return to the Blue Base. According to Tucker, Tex is still pursuing Wyoming, the quest was a failure, and the Alien died. Frustrated that the quest failed and that Tucker did not immediately reveal that Wyoming is still alive, Church orders Tucker to report those kind of events immediately in future.

At the Blue Base, Tucker becomes ill. Church and Caboose discuss Tucker's sickness, which apparently he caught when the Sacred Quest team stayed overnight in a swamp. Church suggests the sword's power source could be giving off radiation. Church and Caboose have a reasonably light and friendly discussion regarding the nature of the sword, as Tucker rolls in pain. This friendly discussion even extends to Church mentioning that he would love to "live in [Caboose's] world for about 10 minutes" just to have some fun.

At the Red Base, Simmons persists in trying to enter the Red Base to relay vital information about the war to the Reds. However, he still meets resistance from Donut and Grif until he very quickly changes out of his mostly blue armor to his original maroon armor. Apparently Simmons learned this ability because of his extreme shyness, which has led him to never use the base's toilet for three years.

Back at the Blue Base, Church and Caboose question Andy on what might be causing Tucker's sickness and suggest that he, being a machine (and thus not able to get sick) go into the base, find out what is wrong with Tucker and report back. Since Andy is a bomb, the only solution he can provide is to blow up the base with Tucker inside, killing all the germs and everything around the base in the process. Finally, out of frustration, he tells Church and Caboose that if they want a medical diagnosis, they need to find a doctor. With that, Caboose says to Church "Please don't do it."

O'Malley and Lopez bicker over who should pick up the telephone that is ringing inside their secret lair, while Doc decries their bickering. It appears that all three have survived their encounter with the Alien and that O'Malley has continued in his pursuit of taking over the universe. It would seem from Lopez's attitude toward O'Malley, all those attempts have failed miserably and this has caused Lopez to become quite cynical and disrespectful toward O'Malley.

Simmons manages to enter the Red Base by correctly guessing the weak password established by Grif and Donut. Simmons wants to report the Blues' plans, but Sarge still considers him a traitor and insists on holding a trial with himself as both judge and prosecutor. This trial is quickly aborted, however, when Grif argues that Donut will want to act as a bailiff in hotpants. As a result, Simmons' sentence is summarily commuted to the payment of a hefty fine, to be split between Sarge and Grif.

Meanwhile, O'Malley, Doc and Lopez return to the gulch. As O'Malley approaches the Blue Base, he is greeted with a "warning shot" from Church, who reveals to Caboose that he was actually trying to hit O'Malley. O'Malley accuses the Blues of attempting an ambush, but Church explains that he just wants to establish a few ground rules at the outset: O'Malley is supposed to enter the base, give a diagnosis for Tucker, and then leave. In exchange, O'Malley demands something "mysterious", "frightening", and "pure evil", as well as a 20-dollar upfront copayment. Church agrees and asks Caboose for 30 dollars.

The episode begins with Sarge, Simmons, and Grif racing toward the Blue Base. Sarge worries that, since the Blues have re-established contact with their Command, they may be receiving new intelligence, weaponry, and soldiers to aid in their efforts for the war. Grif, however, suggests that the Blue Command could simply be giving the same "generic" instructions that Red Command has been giving the Reds. Eventually the discussion changes gears and the Reds ponder where Donut could be. Simmons spots him standing next to a rock, talking to something. After taking a look through his sniper rifle, Grif sees that Donut is talking with Lopez.

Back at Blue Base, Church introduces O'Malley and Doc to Andy. An awkward moment for O'Malley occurs when Church notes that Andy had originally been designed to kill O'Malley. Andy feigns an explosion, frightening O'Malley. Church and Andy share a good laugh, while O'Malley is unamused.

Meanwhile, the rest of the Reds gather around Donut and Lopez. Donut reveals that he had taken four years of Spanish in high school, but, from the subtitles provided, he can neither speak it or understand it fluently. Eventually, after Donut fails to communicate Sarge's request to Lopez, Sarge gains root access into Lopez to force him to play back the message from Red Command stored in his memory. Unfortunately, the message, which actually contains the generic instructions that Grif had mentioned previously, is played back in Spanish. The Reds are at a loss on how to translate the message until Simmons mentions that the Blues had a bomb that could translate the message. Although Grif discourages the idea when he reminds them the bomb can explode via remote detonation as the entire team huddles around it, Sarge wants to retrieve it.

While Doc examines Tucker inside the Blue Base, the Reds digress into a discussion on the relative appropriateness of hand to hand combat, sniping, and nuclear warfare. Eventually, Sarge, with Lopez's head in tow, heads out to steal Andy from the Blues.

Doc returns outside to give Church and Caboose his diagnosis of Tucker. After prolonging his explanation of Tucker's condition for dramatic effect, he discloses that he believes Tucker is pregnant, based on the presence of two different heartbeats. Incredulous, Church goes with Doc to confirm the diagnosis, leaving Caboose alone with Andy.

When Caboose has his back turned, Sarge surreptitiously swaps Lopez's head for Andy, leaving Caboose under the impression that Andy had become a "real boy". Shortly realizing that Andy is useless without Lopez, Sarge returns, distracts Caboose, and swaps Lopez's head for a skull. Upon seeing the skull, Caboose believes that Andy has died and, in hysteria, delivers an extended soliloquy lamenting the loss of Andy.

The last episode of season 4 begins as Doc tries to convince an incredulous Church of Tucker's pregnancy. When Doc discloses the truth to Tucker, he does not believe him either, thinking he himself has impregnated someone and invents excuses. Caboose enters the base with the skull, asking for help, proclaiming that Andy is dead. After Caboose explains how he found the skull, Church decides to leave the base.

Meanwhile, Andy plays back the message from Command in English for the Reds. After hearing the generic instructions, Sarge becomes depressed, and while Grif tries to cheer him up, Donut spots Church approaching with Sheila. Sheila then fires, frightening the Red Team, which regroups behind a rock formation. Sarge calls for reinforcements, and Simmons attempts to negotiate a surrender from the Blues. Annoyed, Church explains what has just occurred back at his base. To Church's dismay, Andy lets slip that it is possible for Tucker to be pregnant, as the Alien's race propagates by infecting other lifeforms with parasitic embryos. Caboose then calls Church to inform him that O'Malley has moved to another host as the Reds had been using their radios, and that Tucker had his baby. Higher-pitched Alien speech can be heard off-screen. Church returns to Blue Base, and Donut follows him, wanting to see the baby. Sarge stops him, and orders him to wait for the ship being sent by Command. Donut argues that it could be weeks, even months before the ship arrives. A ship then promptly lands on top of Donut.

Church returns to the Blue Base where Junior, the baby to which a now-comatose Tucker has given birth, is wreaking havoc off-screen. Church and Doc argue about the child until a spaceship crashes into the gulch on top of Donut; Church leaves to investigate. The Reds bicker about rescue plans until Sarge leaves to fetch a rescue device. Church arrives and claims the ship with Sheila's support.

As Church argues with Simmons and Grif, a tapping noise begins to sound from the ship. Sheila abruptly leaves, forcing Church to retreat to the base.

Church attempts to call Vic for reinforcements, but is stalled by an elaborate answering machine system. Meanwhile, the back door of the ship opens, and an unseen entity emerges.

Church finally discovers that Vic's voice mailbox is full. The Red reinforcement who emerged from the ship is revealed to be the Sister of Grif, who by Simmons' theory arrived using the ship's light drive, which caused her and the ship to move forward in time as it was traveling to Blood Gulch. Meanwhile, it is revealed that Donut fell into an underground cave (Waterworks in Halo 2) after the ship crashed on top of him.

As Caboose attempts to see the new Red soldier using the sniper rifle, Church speculates as to what combat skills the reinforcement may have. Tucker wakes from his coma and joins them, immediately identifying the new soldier as a girl from hundreds of feet away. Sister explains to the Reds that, following the death of a Team Commander, Command has promoted a soldier to the position and sent her to fill the new low-level opening. Since Command seems to presume him dead, the Reds decide to hold an impromptu funeral for Sarge.

The Red Team holds Sarge's funeral, each giving a separate eulogy. Grif makes jokes; Simmons announces his campaign for Red leader; and Sister goes on a tangent about death and age. Finally Sarge, disgruntled, is buried alive.

Tucker is introduced to Junior. Meanwhile, Sister reveals that she was told the dead Commander died of an aspirin-overdose. It is explained she is colorblind, and the "Blue guys" were the ones that really sent her. Underground, Donut wakes up and finds two suits of Blue armor.

The Reds argue whether to keep Sister, before Grif secretly decides to rid the team of her before the still-buried Sarge discovers her Blue allegiance. Doc examines Sheila for her random behavior since abandoning Church in episode 79. Grif confronts the Blues and convinces them to take Sister. Simmons appears after trying to dig up Sarge, and proclaims him missing.

Church gives Sister an orientation, before Tex arrives. Meanwhile, Simmons explains that he discovered a large cavern under Sarge's grave.

Grif and Simmons decide to enter the cave. Meanwhile, Tex is firing at the Blues to try and deduce who is being possessed by O'Malley. Church starts to suspect that Sheila is possessed by O'Malley, causing her malfunction. Tex notices Sister, and reacts jealously.

Soon after Sarge awakens underground, Donut discovers him. As Tex and Sister talk, Church and Tucker discuss having two girls at the base. Back in the cavern, Donut points out what he believes to be a subterranean Blue base, the two bodies he found earlier, and a vehicle resembling the "motorcycle" he stole from O'Malley. Simmons and Grif reestablish radio contact with Sarge, and decide to meet.

Simmons and Grif are shot with projectiles which resemble tranquilizers in effect while waiting for Sarge and Donut. The Blues decide to reboot Sheila.

Doc decides to give Sister a physical. Donut and Sarge find a briefly unconscious Simmons who explains that his attackers have apparently taken Grif with them. At first reluctant, Sarge decides to go help find Grif after realizing his prized shotgun was taken too. Using a tracking device in Grif's armor, they discover he is about a tenth of a mile away and head to find him. The Blues decide Caboose will distract Sheila while Tex shuts her down.

Tucker and Junior overhear Doc's inspection of Sister. Meanwhile, the Reds find Grif, who claims that he was questioned by his captors. As the Blues reboot Sheila, the tank shuts down just before revealing O'Malley's new host to Caboose.

The Blues decide to transfer Sheila's intelligence to the crashed ship's on-board computer. Grif recounts his interrogation, and how Andy was present and translating for his captors, who are looking for "the kid and the sword".

Tex recounts the events of Red vs. Blue: Out of Mind. When York's presence in the future is questioned, Tex comments that, as part of her division's AI implantation process, his armor's special healing ability might have kept him alive. When it is revealed Wyoming teleported away from her before she could question him, Church remembers Gary's ability to create teleporters, and decides he must be Wyoming's AI, Gamma. Church is then called by Vic and told to attack the Reds via the caves. Meanwhile, the Red team discover a surveillance system watching over Blood Gulch in the cavern.

Church somewhat follows Vic's instructions by sending Doc, Sister and Junior through the caves while Church, Tex and Tucker attack the Red base head on. Tucker gives some unhelpful life advice to Junior before heading off. Caboose stays at the base to ensure Sheila's transfer is not disrupted.

The Reds see the Blues advancing on their base on the surveillance system, prompting them to find their way out of the cavern to invade the deserted Blue base. Caboose asks Sheila, now uploaded into the ship, where O'Malley is, relaying Tex the answer. Tex then confronts Church, calling him "O'Malley." Doc and Sister head through the caves, where they find Lopez's disembodied head.

Sarge calls Command for reinforcements, and Simmons hears an echo and leaves to investigate. He traces Vic Jr.'s voice back to the surveillance monitors, and as Simmons' voice is heard, he quickly hangs up on Sarge; the Reds assume the equipment is interfering with their radio signals. Meanwhile, Caboose explains that Sheila said O'Malley was inside the "Blue Leader." Church protests that he was never officially promoted to that position, and is not O'Malley's host. In the caves, Doc, Sister and Junior are approached by a new Alien and his partner, a revived Captain Butch Flowers, now host to O'Malley.

The Blues at Red base are ambushed by Wyoming, and Church attempts to secretly call Caboose for help, but he fails to understand. The tank nevertheless leaves for the Red base, unmanned. The Reds find Andy in the caves, who explains that the New Alien revived Captain Flowers, and begins to explain why O'Malley and Wyoming want Junior before the Reds cut him off by leaving. Tex engages her camouflage to escape Wyoming, and the tank arrives, but is revealed to be controlled by Gary.

Caboose deduces that he must leave Sheila to help his teammates at Red base. Meanwhile, Tucker finds out that Wyoming has the ability to loop time, having gained it from the AI implantation process, just like Tex's camouflage and York's regeneration. By rewinding events until he is victorious in battle, Wyoming is able to detect the invisible Tex before she attacks and kill Caboose. Tucker uses his knowledge of the loop to impale Wyoming with the sword, and save his teammates. When told of the loop, Church wonders if copies of Wyoming were made, as they were when he time-traveled, when the two come across multiple Wyomings.

Flowers/O'Malley and the New Alien are revealed to be holding Doc, Sister and Junior hostage at the underground surveillance system; Flowers mentions to Vic Jr. the plan to give Junior the sword in order to grant him unstoppable power, and that the New Alien is oblivious to their plan. Meanwhile, Church and Tucker manage to escape most of the Wyomings as the time loops continue, which Tucker states that he is aware of because of his possession of the sword, according to Wyoming. Gary is disabled after Tucker connects him to Sheila, and she traps the enemy AI behind a firewall, halting the time loops and the production of new Wyomings. The Reds decide to enter the battle in the Warthog (complete with the classic Tejano music), and take out all of the Wyomings but one. The plan is then revealed: Junior is to become the ruler of the alien race, and O'Malley plans to infect him to exploit their entire civilization in order to "win the war at any cost." Wyoming says that Tex will aid them now that she knows of the plan, and to Church's disbelief, she announces herself on an open radio channel, taunting O'Malley to "come and get her."

Official Ending - Tex reasons that ruling the Aliens would win the war. Church, arguing O'Malley can't be trusted in a deal, begins broadcasting on an open channel to prevent O'Malley from jumping into Tex. As Tex kills the last remaining Wyoming, O'Malley accidentally infects Simmons. Tex knocks Simmons out, and follows O'Malley into Caboose's mind. Church approaches the Reds and warns them to disable the ship so that O'Malley can't escape, before entering Caboose as well.

Inside Caboose's mind, Church finds Tex and O'Malley negotiating their deal to rule the Aliens. He kills them both, causing them to leave Caboose's mind. After killing himself, Church emerges from Caboose's head to find that in the interim Tex has taken the sword, while Junior and the New Alien have boarded the ship.

O'Malley then infects Donut. Tex then knocks him out forcing O'Malley to jump to a different host. After jumping to multiple hosts, O'Malley jumps back into Tex and boards the ship to escape. However, Sarge has placed Andy on board, and gives the order to detonate. The ship disappears, followed soon by an explosion.

Official Ending - Alarm

The Blues retreat to their base. Some time later, the teams loosely echo each other's episode 1 dialog, before Sarge calls the Reds to name a new ATV he built.