In order to celebrate Otis' birthday the animals trick Farmer into going to Turnip-Con for the weekend. However his plans hit a snag when that very same weekend the Beady's nephew, Eugene, comes for a visit.

After Otis saves Duke's life by pushing him away from a falling amplifier, Duke begins getting loyal to Otis and becomes devoted to helping Otis doing everything, but Otis soon becomes annoyed when Duke goes overboard.

The animals are unable to have Saturday night parties because of the farmer constantly weeping about his lost wife. Otis finds him the perfect girlfriend to make him feel better, but they then realize that she is trying to get rid of the farm animals by kicking them out of the barn and take it over (forcing the animals to stay in the hen house which explodes because of the max capacity of the animals in there). So they dress Pig as rich man to lure the woman away from the barnyard, but Pig wouldn't lie and he confessed to her, which makes the woman leave the farmer. In the end, the animals get to have their Saturday night parties, Pig is heartbroken (which he stops after a few minutes), and the farmer went on a cruise with some ladies.

To get revenge at Bessy's insults, Otis tries to humiliate and embarrass Bessy, but at every attempt, the prank backfires. Bessy subsequently gives Otis a real (and humiliating) prank that ends up him and Pip covered in honey and seeds.

This week's Moose Appreciation Week, so Otis disguises himself as a moose so he can get positive attention from humans, but his plan goes awry because the week is over and now the Moose HUNTING SEASON starts today and now Snotty Boy and his friends are trying to hunt him down, and his antlers are stuck to his head. So the animals rigged a robotic moose to scare Snotty Boy away from Otis. But Snotty Boy accidentally goes out on a busy road. So Otis has to save him from being hit by a car. Because of his heroism, the county now bans Moose Hunting Season and makes it Moose Appreciation Week all year long.

Upon realizing how lame his friends are: Freddy and Peck dressing him up as a bunny instead of a monster to scare away crows, Abby inviting him to bingo, and his friends habits at bingo (Pip's loud keyboard typing, Duke's squeaking his toy, Abby's slurping on a drink, and Pig digging in his ear), Otis ditches them and goes out for a night on the town, pulling pranks with the Jersey Cows. Otis, unfortunately, ends up getting arrested. So now his friends have to come get him out and stop the police officer from taking him away again.

After the gang notices a distinctive birthmark on Pig's backside, Pig starts to believe that he is related to the royal Pampered Pigs. After training Pig, he becomes snobbish to his fellow companions.

The animals become pop stars when Pip broadcasts one of their sessions, but soon their egos begin getting out of control and begins to put a damper on their friendship, which eventually causes a heartbroken Peck to quit.

Freddy tries to hide his non-carnivore ways from his parents, who are invited to a birthday party at the farm, and Freddy tries to make sure they don't eat anybody, including Peck, while keeping it a secret to his friends.

After Snotty Boy returns to torment the animals, Otis accidentally falls on him and becomes unconscious. Luckily, he's got a pulse and they decide to take him back to the Beady's, but Abby says that Mrs. Beady will blame them. Otis sends a disguised Pig over to the Beadys' as Snotty Boy so they don't get suspicious. But Pig enjoys being Snotty Boy so much that he decides to stay as him forever. Meanwhile, Snotty Boy gets amnesia and the animals realize that the only way to get Pig back is to turn Snotty Boy back to his old mean, obnoxious jerky self so Mrs. Beady will recognize him and because Snotty Boy is annoying them with his newly found kindness and sweetness.

Otis discovers that he has the same bell as Bessy's long lost child, so Bessy believes that Otis is her child, so she starts treating him like a child and humiliates him and refuses to let him goof around and do pranks on Mrs. Beady.

Otis loses the saloon to Chubs Malone, head of the gopher underground, in a game of Fizzbin. Now, the gophers dominate the barn at night.

Bigfoot is sighted in the woods, and Otis decides to go hunting for him, but Abby finds him and brings him to the barnyard for his protection. Mrs. Beady, however, is out to capture Bigfoot and prove she is not crazy.

Otis and his friends dress up as girls because the bowling alley is open, but only girls get to go free. Their plan backfires when Snotty Boy and his friends try to take them out on a date. They are forced to agree when they realize that Abby and Bessy have put glue on their women's clothes so that they can't take them off and they can't throw them off because Pip removed the stink bomb from the purse to make room for himself. After one night, the other animals couldn't take it anymore, but Otis still continues to go out as a girl so he can get free things from Snotty Boy. Everything goes well until Otis realizes that Snotty Boy has engaged to him.

Pig returns to his birthplace to be married, but after Otis realizes that Pig's bride, Brunhilda, is cruel and bratty, he tries to stop the wedding by beating Pig in a contest.

Otis is bored of Abby's book club, so he releases Wild Mike from a cage so they can have a dance party, but things get out of control when Wild Mike accidentally escapes the barn and is captured by humans to use on a dancing TV show.

When Otis accidentally blows up the barn with an atom smasher he accidentally received in the mail, they audition for "Bling My Barn," a home improvement show that fixes up barns for deserving families. But when they dress up Pig as a baby, he discovers the perfect family they're competing against, he tries to warn the gang but they ignore him thinking he's throwing a tantrum, so he runs away forcing them on a wild goose chase to catch him. When they finally caught Pig, he shows them the perfect family, so they drop out of the contest and use the material from the farmer's house to rebuild the barn.

In order to get out of going to a "Brianna Texicanna" concert with Abby so he and his friends can go bowling to beat a rival farm, Otis lies and says he needs to celebrate "Happy Animal Fun Time Day" in which everybody must stay home to celebrate. But Abby believes him and decides to cancel going to the concert and stay home to celebrate too. So Otis distracts her with the holiday's activities so that he can join with his friends at bowling and Abby doesn't see that he lied to her.

When Otis injures himself, Pip temporarily takes over as the barn leader, and when he recovers, realizes that the others think Pip is a much better leader than Otis was. Insulted, Otis decides to leave the barnyard and be a leader where he's needed – with a den of beavers.

Otis is too lazy to do chores around the barnyard so he creates a clone of himself to do the work for him. It turns out the clone is a much smaller version of him, and when Mrs. Beady ends up capturing the clone, she is set to take him to a TV show so she can prove that animals can talk.

When Snotty Boy's cousin Bernard stays at the Beady house and torments Snotty, he escapes and tries to seek refuge in the barnyard, so the animals must help Snotty to defeat Bernard so then he could leave.

When the animals go on a camping trip, Pip tells a scary campfire story about a witch. When they get lost and find an old woman's house with tons of sweets, Otis fears that this woman is indeed the witch from Pip's story.

When Pig cooks up what appears to be permanent glue, the animals try to sell the glue to make money. They soon realize that the glue explodes two hours after it is applied and must find a way to get rid of it safely. When they found all the glue from all the buyers, they realized they sold 500 pounds of glue to city hall so that the town can use it to patch the town's cracked manure tank. So the animals race to dispose the manure tank before it floods the town with manure.

Otis is knocked out and wakes believing that he is King Cudenhotep. The only way for him to get back to normal before the farmer comes back is if someone knocks him in the head again, but Otis has beaver guards that prevent others from getting too close to him. When they finally turn Otis back to normal, the farmer see them but get hit on the head believes he is Ben Franklin.

Duke wants a playmate, but no other animal wants to play with him, so the animals convince the farmer to get Duke a playmate. Unfortunately for Duke, the farmer brings Duke's arch-rival Baxter back to the farm, and Baxter causes trouble with the farmer while blaming everything on Duke, getting Duke in trouble and being put in the barn with the other animals. They try to stop Baxter but the farmer scolds them for hurting him. So they dress Otis as a bear so that Baxter pushes the farmer to it and get Baxter in trouble. The plan works but Duke accidentally attacks a real bear instead because Otis was late on cue.

Pig has been hanging out with his imaginary friend, Mr. Wiggleplix, for weeks and it drives the other animals crazy. Then one day, Pig claims that Otis killed Mr. Wiggleplix so Otis has to dress up as Mr. Wiggleplix for Pig to feel better. Things take a turn for the worst when Otis says he is leaving for a magical land but Pig believes it and wants to go with him. All of the sudden, the real Mr. Wiggleplix comes alive and stops Otis from impersonating him.

Otis convinces his college buddies Donner and Blitzen to stop by the barnyard on Christmas Eve. During the visit, Otis accidentally gives Santa a cup belonging to Freddy, who is sick. When Santa comes down with Ferret Fever and can't finish his rounds in the county, which turns out to be his last stop on his Christmas Eve rounds, then Otis and the animals vow to make toys and deliver them by midnight to save Christmas. Meanwhile, Snotty Boy, not knowing he’s on the naughty list, really wants a Red Rider BB Taser that Santa doesn't bring him every year. So he sets a trap for Santa to make sure he brought his present.

After Freddy gets struck by lightning, he becomes a genius and knows everything, so they get him to compete in a trivia show so they can win a million dollars. They realize that, unfortunately, Freddy's intelligence is only temporary and he becomes stupid again after a prolonged period of time. So the animals make an electrical system to make Freddy smart with each shock. But the problem is, every time a question is announced, he keeps getting dumb again and again. Frustrated that he keeps getting dumb, Freddy goes backstage and shocks himself at high velocity and dreams that he meets with Albert Einstein who gives him the answer to the final question which is actually incorrect so Freddy curses Albert Einstein for making him lose.

Duke is excited when his sister Stamps comes to visit, but is shocked when he realizes that Stamps is engaged to his arch-enemy, Baxter. However, the animals learn that Baxter is after Duke and Stamps' uncle's priceless dog bone collection. When they try to frame Baxter for chewing up a couch at his bachelor party (so that Stamps will dump him because she hates couch-chewers), Duke beats him to it and now scolded in front of Freddy and Peck. So at the altar, Duke tells Stamps about Baxter going after the dog bone collection, she dumps Baxter and he is launched in the field.

The farmer is in love with a woman named Branco Betsy who's a rodeo host and is interested in bull riders, so Otis pretends to be the farmer's bull so Branco Betsy would be impressed. At the rodeo, however, Otis meets Psycho, a much bigger bull, who injures him, so now the farmer has to ride Psycho, the big (and dangerous) bull.

Mrs. Beady has no choice but to move with the barnyard animals after being kicked out of her house and being mistreated by Mr. Beady's mother, Mother Beady.

The animals climb a mountain to reach Bigfoot's home after Bigfoot gets in an accident.

The clones Little Otis and Little Abby come back to visit the barnyard, but it becomes a problem because they never sleep so the animals couldn't sleep when they're here. In order to make them stop visiting, they try to create mini-clones of Pig, Pip, Freddy, and Peck so Little Otis and Little Abby can have friends. A problem arises when the owner of the Clone-a-torium plans to use the clones to expose the humans so they would know that animals can talk, and Otis and his friends must stop him from doing so.

While trying to escape Snotty Boy, the animals run over Snotty's clown father. His dad survived, but has lost a lot of hilarity and Pig takes him into surgery. Otis disguises himself as Snotty's father to distract him while he recovers and becomes a cool dad to Snotty Boy. Only Snotty comes to love and admire Otis in a way he never did for his lame clown father. Otis has to think fast before he ruins this miserable family.

Otis and his friends become cops after another cop gets injured, and they try to solve a crime that is about stealing in a donut store. They find the suspects are Mrs. Beady, Snotty Boy and the Farmer. They try to interrogate them, but they're all innocent. They then learn that Pig is the real thief because he wore a burglar costume every time he goes to get donuts for his friends.

In the series finale, Otis orders a satellite dish online in order to watch monkey boxing from Rio. Mrs. Beady sees this and believes that he is secretly signaling Aliens. Otis finds out and tries to prank Mrs. Beady with a fake alien invasion broadcast. This broadcast is sent to real aliens who are attracted to Earth and plan to conquer and destroy the planet. The animals must stop and stall them while they figure out their weakness.