The third season begins with Phineas and Ferb building a gigantic biome during a bit of bad weather to help Isabella earn a Fireside Girl patch.

For Harbor Days Festival, Phineas and Ferb celebrate by creating a mechanical version of the historical elusive shark of Danville Harbor. Seeing what the boys are up to, Candace enlists some help to capture the mysterious shark. Meanwhile, Dr. Doofenshmirtz invents the 'Salt Water Taffy-inator' to give cavities to every kid in the Tri-State Area.

Inspired by the lost verse from the nursery rhyme, "Hey, Diddle Diddle", the boys decide to take some cows to the moon to see if its low gravitational pull actually does produce the best tasting ice cream ever. Back at home, Candace decides to take advantage of the boys being gone and attempts to make a fancy dinner for Jeremy, but her lack of cooking skills don't add anything to the plate. Meanwhile, Dr. Doofenshmirtz attempts to use his 'Moisture Suck-inator' to turn his neighbor's plants brown, so that his plants will be greener by comparison.

Candace gets a bad haircut and must rely on Phineas and Ferb's hair growing machine to correct it before she attends the Endangered Animal Benefit with Jeremy and his mom. However, when Candace turns up the power, her hair grows much more than expected and she is mistaken for a rare tangerine orangutan. Meanwhile, Dr. Doofenshmirtz is developing his Very, Very 'Bad-inator.'

When Dr. Doofenshmirtz thinks Vanessa overhears him say he would rather have a son to do his evil bidding, he feels terrible so he intends to zap her with the "Forget-about-it-Inator." Meanwhile, Norm shares his feelings of wanting to be a real boy with Dr. Doofenshmirtz and decides to play up the "son" role. Back at the Flynn-Fletcher household, Candace has Stacy hypnotize her into ignoring the need to bust her brothers so that she can spend the entire afternoon relaxing with Jeremy, but unfortunately the hypnosis trigger words end up playing right into her date with Jeremy.

After Candace injures her ankle and is told to stay in bed, she drives herself crazy trying to get her Mom's attention in order to bust her brothers. Fortunately, Phineas and Ferb provide her with a box of items to stave off her boredom. However, it ends up being more of a hindrance, until she unknowingly helps the boys warn their cosmonaut friend about a dangerous obstacle approaching them. Meanwhile, Perry interrupts Dr. Doofenshmirtz's Chicken Soup themed escapade.

Phineas and Ferb enlist the help of cyclist Greg LeMond to help Baljeet compete in a bicycle race. Meanwhile, Doofenshmirtz tries to bring the city to a standstill so he can bid on an auction unopposed.

Phineas and Ferb build a giant version of a favorite childhood game, with Danville as the central location. Meanwhile, Doofenshmirtz takes Vanessa on a camping trip.

When Ferb's cousins visit from England and challenge him to a soccer match, he and Phineas warp the walls of physics and build a high tech 3D stadium. Meanwhile, convinced that her relationship with Jeremy depends on her being more proper, Candace enlists the help of Ferb's British cousin, Eliza, to teach her the rules of etiquette. Back at Doofenshmirtz Evil Inc., Dr. Doofenshmirtz is sick in couch but forces himself to set off his \"If-A-Tree-Fell-in-the-Forest-Inator\", which causes any tree that falls to say his name.

Potato gremlins appear all over town when Phineas and Ferb clone a potato chip from Buford and it mixes with his DNA; Doofenshmirtz tries to summon the Spartan army with his historical army retrieve-inator.

Phineas and Ferb create their own language, Ferb Latin, which quickly catches on. Unfortunately for Candace, she awakes from a massage puzzled to find everyone else speaking a language she doesn't understand. Meanwhile, Dr. Doofenshmirtz decides to use propaganda as his new "-inator," believing that it will work since people will believe anything they read.

After locating and retrieving the Amulet of Juatchdoon, adventuring archeologist duo Ohio (Phineas) Flynn and Rhode Island (Ferb) Fletcher set off to South America to help Damsel in Distress Isabella find the Lost Temple of Juatchadoon and her missing mother. However, Dr. Doofenshmirtz has other plans for the amulet - to awaken the evil corn colossus to give him the power to destroy the world.

After losing a gift that Jeremy made for her, Candace is determined to recreate it before Jeremy realizes it’s missing. Unfortunately, Candace can’t remember what it looks like, so she enlists Phineas and Ferb to use their mind machine to enter into her subconscious and recapture the memory. Meanwhile, Doofenshmirtz’s evil plan is to use his Underwear-Inator to take over the Tri-State Area, since everyone's greatest fear is being caught in public in their underwear.

Thinking it would be cool to be part of an ant society, Phineas and Ferb create and infiltrate the Antius Maximus, a massive ant farm filled with giant ants. Suspecting that the boys are up to something, Candace accidentally drenches herself in the ant pheromones and follows them inside. Meanwhile, Doofenshmirtz feels tired and lethargic after eating turkey and decides to create a Turkey-Inator that will create a sleeping epidemic in Danville by turning things into giant irresistible turkeys.

Inspired by Ferb's personal anti-gravity device, Phineas thinks it would be fun to suspend trampolines all over Danville.

After Mom asks the kids to keep quiet while she prepares for her online knitting test, Phineas and Ferb create ninja outfits designed to hide the wearer from anyone who is not wearing them. Meanwhile, Candace becomes increasingly frustrated after she can’t find the boys and bust them. Across town, Dr. Doofenshmirtz invents the De-Handsome-Inator.

Brigitte, Josette, and Colette, the visiting Fireside Girls from France, help Isabella capture the American Grizzly Bear, one of the world's most dangerous creatures. Buford's plan to jokingly dress up as the bear backfires when he discovers the identity of Brigitte, throwing him off his game. Back at their grandparents' cabin, Phineas and Ferb create the most amazing "run-through-the-sprinkler" experience. Meanwhile, Dr. Doofenshmirtz's loathing of pretzels drives him to create the "De-Twist-Inator" to untwist every pretzel in Danville.

With Fall around the corner, Phineas and Ferb decide to invent "S'Fall", a colorful world full of giant leaf piles and gourds. Meanwhile, over at Evil Inc., Dr. Doofenshmirtz is mentoring Rodrigo, a budding student of evil. Unfortunately, Rodrigo truly is evil, and when he captures Dr. Doofenshmirtz and Agent P., it’s up to Major Monogram's son, Monty, to save the day.

Phineas and Ferb create their own flying saucer to help solve the mystery of a recent rash of crop circles. Meanwhile, Candace tries to give up her tattling habit by taking a "me" day, and across town, Dr. Doofenshmirtz challenges the local pizzeria's "37 Minutes or it's Free" rule by using his "dough-blow-inator" to generate a powerful current of air to hold the pizza dough aloft indefinitely.

The guys help their dad unearth a missing piece of Danville history; Doofenshmirtz tries to make himself younger to win a children's film festival.

Candace finds it difficult to bust Phineas and Ferb when her brothers build nanobots that can assemble into any object they can imagine. Meanwhile, Dr. Doofenshmirtz has jury duty, so Norm takes over the day’s evil scheme -- to destroy Danville by using weapons.

The Flynn-Fletchers are off on an African safari, leaving Perry at home to deal with Doofenshmirtz and his most evil plot yet: to take over the O.W.C.A. But when Doofenshmirtz accidentally zaps Carl the intern with his Ultimate-Evil-Inator ray, Carl takes over the O.W.C.A. (Organization Without a Cool Acronym) and imprisons Doof and Monogram. Agent P steps in but gets zapped with Doof’s many rays and in the cliffhanger of all cliffhangers, disappears.

Agent P's fate is finally revealed in the action-packed finale of the two-part television special that left Phineas, Ferb and the gang hanging...literally off an unchartered gorge and Candace frantic over a phone call with Jeremy that left their relationship status in limbo. Now, with Agent P nowhere in sight, Dr. Doofenshmirtz and Major Monogram square off against evil Carl who controls a set of familiar-looking robots to take over the OWCA, in one of the biggest battles yet.

When one of Dr. Doofenshmirtz's "-inators" zaps him and Agent P into the middle of nowhere, they must embark on a comical journey filled with twists and turns to return home.

Candace is put in charge of Phineas and Ferb just before they seize the opportunity to make the most of Danville's electricity blackout while Dr. Doofenshmirtz tries to use pity to his advantage.

Buford removes a part from a tire swing the boys are building and it accidentally shoots a ray that turns Candace into a fly. Meanwhile, Doofenshmirtz is suffering from evil scientist’s block.

Candace challenges Buford to keep Phineas and Ferb’s invention from disappearing so that she can sweep in and casually bust her brothers. Across town, Doofenshmirtz has had one too many lattes and is experiencing an extra burst of evil energy.

The boys create Rutabaga-themed vehicles when Candace is chosen to be Rutabaga princess and gets to start the "Running of the Chinchillas." Across town, Doofenshmirtz plans to turn himself into a real live Kinderlumper to scare Roger into relinquishing control of the Tri-State Area over to him.

Perry comes face to face with an Australian platypus hunter set on destroying him. Baljeet is having an existential emergency and finds himself incapable of making decisions.

When Candace thinks Jeremy is bored with their usual hangouts, she sets out to find something unique to do with him. Meanwhile, Phineas and Ferb power through town surfing on a giant ball of water and Doofenshmirtz plans to use his Double-Negative-Inator to confuse his local eatery into giving him a wintery drink that is usually not served during summer.

When Pinky goes missing, Phineas & Ferb create a machine that will amplify Buford’s senses to those of a dog’s. However, it works so well that the animal agents’ secret identities are put in jeopardy. Meanwhile, Candace tries to meet up with Jeremy for lunch at City Hall but gets stuck in a mandatory tour.

Candace and Stacy compete in Phineas and Ferb’s Ultimate Obstacle Course. Doofenshmirtz plans to humiliate his brother, the Mayor.

The gang switches bodies with alien tourists for a free intergalactic vacation.

Inspired by Candace's book club selection, The Iliad, the boys reenact the Trojan War -- but with a Phineas and Ferb twist. Meanwhile, Perry discovers that Doofenshmirtz has a major problem with throwing things away so he helps him find his De-Clutter-Inator.

Agent P travels to the glamorous city of Montevillebad to stop Doof from winning the Grand Prix and collecting the prize money. When Doof uses his "I-don't-care-Inator" to sabotage the race and eliminate the competition, including international racing legend of Italian-Scottish-Swiss-Dutch descent Paolo Vanderbeek (Patrick Dempsey), Agent P must take the wheel and go head-to-head with Doof on the racetrack.

Doof's latest inator changes the way the Earth moves and it is up to Phineas and the gang to save summer.

Phineas and the gang help Love Händel prove the existence of Klimpaloon, the magical old-timey bathing suit that lives in the Himalayas, to verify that their song, "The Ballad of Klimpaloon", is legitimate.

Candace is accidentally hit by the Impersonator-inator which changes her appearance to a pizza delivery guy, but uses this appearance to help her better understand boys.

In a parallel universe far, far away, Phineas and Ferb are tasked with returning the Death Star plans to the Rebel Alliance before Storm trooper Candace catches up to them. Meanwhile, complications arise when Perry is trapped in carbonite.

Doofenshmirtz's latest "inactor" turns Danville citizens into contagious zombies. Agent P. and the gang try to save the town and avoid becoming zombies themselves.

After Doofenshmirtz is defeated, a new threat in the 2nd Dimension emerges, leaving it up to Phineas, Ferb, Candace and her resistance fighters to defeat this new foe.

It's the last day of summer vacation and Phineas and Ferb decide to seize the day and make the most of it. Unfortunately for Candace this means it's also her last chance to bust her brothers... or is it?