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.

Candace realizes that she needs to spend more time with Stacy, so she vows to spend the whole day with her only. But while visiting Jeremy and his mom, Mrs. Johnson, Dr. Doofenshmirtz's "combine-inator" zaps her and Jeremy, literally joining them at the hip. Meanwhile, Phineas and Ferb build a giant robot dog that causes a lot of mischief.

Phineas and Ferb's newest invention is a pair of boots that make the wearer extraordinarily fast. Candace decides to wear them so that she can be in two places at once; at Jeremy's family picnic, where she runs into Mrs. Johnson, and also at the library where she promised Mom she would read to the kids. Meanwhile, Dr. Doofenshmirtz's building is put up for sale so he tries to convince a prospective buyer, Annabelle, who turns out to be a long lost relative of the Johnson family, that it is not worth buying.

While visiting their grandparents, the kids decide to create and race a giant hot air balloon. Meanwhile, Candace is inspired by train engineer Glenda's can-do attitude and decides to "give up" on busting her brothers. On the other side of town, Dr. Doofenshmirtz finds a Dodo bird egg and is convinced that it is a fierce bird-monster that can help him take over the Tri-state area, but discovers the exact opposite when the egg hatches.

It's Phineas' birthday and for the special occasion, Ferb puts together a clip show of the gang's favorite moments. Meanwhile, Agent P has to stop Dr. Doofenshmirtz from using his 'non-inator' to pre-empt his brother's biography from appearing on television.

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.

When Candace discovers that Phineas and Ferb have invented a computer that can answer anything, she asks it how she can finally bust her brothers once and for all. Meanwhile, Dr. Doofenshmirtz loses the key to his latest invention, the "All Purpose-inator," and Agent P must find it before he does.

Perry misses his 100th battle against Dr. Doofenshmirtz when Candace takes him to the Charity Pet Wash with her. Perry's absence goes unnoticed when the zookeeper's typical platypus at the Danville Zoo stops Dr. Doofenshmirtz's plan to zap his brother with his "Least Likely-inator." Meanwhile, the boys build a fun house Phineas and Ferb style.

Candace has no choice but to go to her brothers for help after she loses her phone for the fifth time. Unbeknownst to her, the phone that they invent for her has a voice activated phone transfer app that sends her to Easter Island. Meanwhile, back at Evil Inc., Dr. Doofenshmirtz invents a "Pick 'Em Up-inator" to pick Vanessa up from class, then he finds Sarcastic Norm Head, the Norm head prototype that has an affinity for sarcasm, later Doofenshmirtz and Perry watch an exercise show.

Inspired by Dad's favorite childhood program, the boys decide to create a magic carpet, and Candace is convinced that fortune cookies will lead her to bust her brothers. Meanwhile, Dr. Doofenshmirtz plans on ruining his brother's art unveiling by using his "Stain-inator" to ruin a mysterious painting, but as it turns out, the painting is Dr. Doofenshmirtz's very own masterpiece that he created when he was a youth back in Gimmelshtump.

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.'

Mom joins Jamie Oliver as one of the judges for Danville's Meatloaf Festival Cook-off, as he stresses healthy eating and fresh ingredients. Meanwhile, Candace puts a bid on a prized souvenir resembling band members Nigel and Adrian from her favorite band, Tiny Cowboy, at the Rock and Roll Memorabilia Auction, but gets distracted when her brothers build a bounce house in their backyard. On the other side of town, Dr. Doofenshmirtz has plans to enter his family meatloaf recipe into the competition using "hate" as the special ingredient.

When Mom tells Candace she wants to spend the day with her, Candace spends the entire time with her in the backyard so that she can bust her brothers. Unfortunately, Phineas and Ferb's grand plan for the day only entail watching the grass grow after getting zapped by Dr. Doofenshmirtz's Dull-and-Boring-inator earlier that day. Meanwhile, Agent P partners up with Dr. Doofenshmirtz to fix the now destroyed Dull-and-Boring-inator into a Dynamic-inator in order to fix Phineas and Ferb.

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.

On the last day of the Flynn-Fletcher family road trip, Candace thinks she’ll finally have a couple of hours to relax and not worry about busting her brothers. However, Phineas and Ferb decide to build a truck stop diner on top of the RV. Meanwhile, Doofenshmirtz is also doing a road trip, but he’s using a big rig to transport his boom juice across the Tri-State Area.

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 Lawrence heads out to attend a speaking engagement on antiques, he unwittingly finds himself participating in the L.O.V.E.M.U.F.F.I.N. Pageant of Evil against Dr. Doofenshmirtz and Rodney. As a special host oversees the proceedings, Perry is tasked with monitoring the situation, but Lawrence gets hit with Rodney's "Make-Everything-Evil-Izer", and is crowned the supreme leader of L.O.V.E.M.U.F.F.I.N. Meanwhile, Candace is determined to bust the boys but doesn't realize that the object she's looking at is not theirs. Across town, the boys are playing a giant game of darts.

It's Halloween night and the kids encounter a strange boy named Russell who is convinced his house is haunted. Meanwhile, Dr. Doofenshmirtz's disdain for grass causes him to invent a "mind-transfer-inator" enabling him to merge minds with a cow and destroy all the grass in the Tri-State Area. Unfortunately, his plan backfires and he transforms into a scary "were-cow" that wreaks havoc any time there is a full moon. It's now up to Agent P to stop him and save Danville.

Candace is bitten by a bat after watching a popular vampire movie with Stacy and worries that she is becoming a vampire. Phineas and Ferb's latest gadgets lead Candace to believe that she has indeed made the change from teenager to teen vampire. Meanwhile, Dr. Doofenshmirtz plans to change the Tri-State Area into a carbon copy of Gimmelshtump so that it will be easier to take over.

When Phineas and Ferb are inspired by an antique escape chamber that Dad acquires, they decide to build a computer-controlled tower that will trap them inside and allow them to explore the world of escapement. Meanwhile, Dr. Doofenshmirtz invents a "Rude-Inator" to ruin Roger's meeting with a visiting dignitary from England.

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.

The boys decide to put on a traditional family Christmas special featuring their family, friends and a few very special guests, including Grammy winning recording artist Kelly Clarkson (playing herself). The episode features three new holiday songs - Isabella's "Let it Snow", a Buford and Baljeet rendition of "Good King Wenscelas" and the whole gang singing "We Wish You a Merry Christmas".

It’s the Stone Age and Phineas and Ferb are cavemen who decide to invent something new, fun and useful…the wheel! Meanwhile, Dr. Doofenshmirtz attempts to make his digs more upscale by using the precursor to the Inator device... a plain old stick.

In ancient feudal China, Princess Isabella is part ruler and Master Perry has given up the way of the warrior. After Phineas and Ferb witness Doofus Khan capture the Princess and take her as a prisoner, they track down Master Perry and convince him to teach them his warrior ways so they can rescue Princess Isabella and save China.

During medieval times, Phineas and Ferb (or, Ferb-a-lot) set off on an epic quest to find the legendary sword, Excaliferb, so they can defeat the evil sorcerer, Millifishmirtz.

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.

Craziness has ensued in Danville and no one has any idea what’s going on. The wackiness unfolds when Phineas and Ferb create Cheesetopia, Doofenshmirtz makes Perry his butler with his Butler-inator, and Carl is trapped by Doof while in a squirrel costume. All is explained, in an episode of Phineas and Ferb that starts at the end and works its way back to the beginning.

When Phineas and Ferb can’t find Perry, they decide to create the Perrytronic 3000, a mechanical structure that can assume any form. Of course, being aware of the boys’ every move, Candace decides to take a different tactic on her busting approach by using a new technique that keeps Phineas and Ferb from finishing their Perry project. Meanwhile, Doofenshmirtz invents a Duplicator-Inator-2 so that he can duplicate his own head and make himself twice as smart.

The executive of Totally Tools oversees a contest to find the company's \"spokesanimal\", and Perry is crowned the winner. However, the victory puts Perry's secret identity in jeopardy, forcing Major Monogram to appoint Agent S as a temporary replacement, but when Dr. Doofenshmirtz sees his new nemesis is Sergei the Snail, he mistakenly underestimates his new opponent. Meanwhile, Candace has been welcomed into Mandy's "Stop the Busting" retreat, which aims to teach Candace to control the urge to bust her brothers through positive reinforcement.

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

Baljeet announces that he is no longer Buford's nerd, and Buford is heartbroken.

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.

When Mom is out of Doonkleberries for her famous Doonkleberry pie, the boys set out to find some for her. Meanwhile, Perry and Dr. Doofenshmirtz find themselves across the ocean as Doofenshmirtz returns home to renew his Druesselsteinian driver’s license. Back in Danville, Candace is convinced she has discovered the answer to her busting problem.

Meap's world is put in danger and the boys try to help him save the universe when they travel to Seattle. Meanwhile, Doofenshmirtz visits former nemesis Peter the Panda.

Paul the Delivery Guy discovers his job has a higher calling to save Danville as he makes stops at Phineas and Ferb's house, Doofenshmirtz Evil, Inc., Danville City Hall and the OWCA, in a special episode seen through his eyes. The rock band, Love Händel, returns for some musical accompaniment. Meanwhile, at Doofenshmirtz Evil Inc., Perry has lost the tools in his hat.

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.

When the boys ask Candace to decide what they should do for the day, she slyly asks them to invent a device to attract their Mom so that she can finally bust her brothers. Meanwhile, Dr. Doofenshmirtz has invented a "Baby-Cry-Inator" designed to tarnish his goodie-two-shoes brother's image with the electorate.

When Baljeet becomes concerned that he is losing his mental edge, the boys invent a cerebral stimulatory hat, or "Brain booster," to help him. But when the hat exceeds expectations and makes Baljeet exponentially smarter, he suddenly views everyone else as beneath him and becomes a threat to civilization by taking Earth's atmosphere and bringing it to the moon. Meanwhile, Dr. Doofenshmirtz plans to use his "Key-Find-Inator" to collect all the keys in Danville in hopes that it will lead to the Key to the City.

Candace's plans to watch over Phineas and Ferb backfire when Dr. Doofenshmirtz's "Babe-inator" turns her brothers into babies. After having an epiphany, Dr. Doofenshmirtz shows up at the OWCA to give up his evil ways. Agent P has no choice but to show Dr. Doofenshmirtz the ropes of the trade, but things quickly sour between the two after Dr. Doofenshmirtz accidentally exposes the identity of a fellow animal agent.

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.

When the boys learn that the famous Crikey the Crocodile has gone missing, they set out to find and return him to his home at the Danville Nature Preserve. Meanwhile, to Candace's amazement, Irving reveals his digital scrapbook compilation of all of Phineas and Ferb's wild creations, and guest star Ray Liotta fills in for Major Monogram to give Perry his mission. Also, Dr. Doofenshmirtz plans to embarrass his brother by using his 'Chicken-Replace-inator' to replace Roger's mayoral award with the nearest chicken.

Candace's plans to hang out with Jeremy are derailed after he becomes interested in playing Phineas and Ferb's newest game, jet pack volleyball. Meanwhile, when Dr. Doofenshmirtz discovers he invents "-inators" in his sleep, he decides to go back into his dreams to find out what is happening.

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.

Candace tries to bust Phineas and Ferb when they put on an enormous backyard magic show, while Vanessa and Major Monogram's son Monty get coffee together despite their warring fathers. Meanwhile, Dr. Doofenshmirtz tries to become hip in an attempt to get youthful followers.

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 accidentally turns into a fluid when she comes into contact with a device that turns solids into liquids. Meanwhile, Doofenshmirtz turns himself into a platypus to defeat Perry in battle.

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.

Phineas and Ferb create their own TV shows and commercials.

After discovering that a strange planet is hurtling directly towards Danville, Phineas and Ferb set out to avert a disaster, while Buford looks forward to making contact with its alien race. Meanwhile, Dr. Doofenshmirtz hopes to steal the world's largest ball of twine.

Phineas and the gang introduce Ferb and Perry to their newest project - training domesticated squirrels to live in the wild. Meanwhile, Dr. Doofenshmirtz aims to do a better job of seeing through his evil plans now that Agent P is back.

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.

Agent P quickly figures out there is more to Norm's odd reality show that celebrates the eventful life of his creator Dr. Doofenshmirtz, which is recreated through flashbacks and special guests.

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.