Phineas, Ferb and the gang are all sick with a cold, so they decide to make it the best "sick day" ever by creating a live television feed to their friends' homes so that they can all enjoy a day of fun together. Meanwhile, Vanessa learns from her mom, Charlene, that her dad is picking her up from a party she is going to with her punk rock boyfriend Johnny and is worried that he will embarrass her yet again. However, Dr. Doofenshmirtz is busy trying to use his "Deevolution-ator" to drain Agent P's will power so that he can control him, and things get out of hand when Dr. Doofenshmirtz picks up Vanessa at the party, and it's up to Agent P to save the day.
Candace accidentally gets hit by Phineas and Ferb's molecular separator ray which causes her to have two different personalities - Romantic Candace and Busting Candace, so the boys have to figure out a way to put her back together again. Meanwhile, Dr. Doofenshmirtz tries to get over his fear of high diving, but he figures that if he can't, he will just use his "Look-away-inator" to zap everyone so that they do not witness his shame.
Phineas and Ferb plan to put Danville on the map by building the world's tallest building. However, Candace teams up with Albert and utilizes his expertise to bust her brothers. Meanwhile, Dr. Doofenshmirtz wants to be responsible for all the evil in the Tri-State Area, and since he believes that evil levels rise during a full moon, he plans to rotate it so that only the infamous "dark side of the moon" faces Earth.
When Linda is asked to do a Lindana reunion concert, Lawrence worries that she might be missing the excitement of her old life, so he asks the boys to help turn him into a pop star so that he can perform at the concert and show mom he too is an exciting guy. Across town, Dr. Doofenshmirtz plans a faux alien invasion in order to take over the Tri-State area.
Phineas and Ferb create a life sized maze filled with fun obstacles. Melissa, the leader of the Little Sparks, a younger branch of the Fireside Girls, is immediately captivated when she meets Candace and finds out that she was a Fireside Girl who earned 50 patches in one day. When the girls try out the maze, Candace takes charge, but things don’t go as planned. Meanwhile, Dr. Doofenshmirtz reasons that if the Leaning Tower of Pisa can generate souvenir revenue, then surely he can use his latest invention, the "Tilt-inator," to tilt buildings so he can sell souvenir replicas.
Phineas and Ferb head to the Tri-State area’s annual sci-fi/comic book convention to meet their hero, special effects guru Clive Addison. Their plan gets sidetracked when they’re swept into a duel between fantasy fans and sci-fi geeks. Meanwhile, Candace tries to keep secret that she’s a fan of Ducky Mo-Mo, another convention staple. Across the convention hall, Dr. Doofenshmirtz has taken television executive Jeff McGarland hostage so he can pitch him a show he’s developed, Doof ‘N’ Puss.
It's the summer solstice, so Phineas, Ferb, and their friends decide to travel around the world in one day in an effort to create the "biggest, longest, funnest summer day of all time". But not everyone believes they can actually achieve what they have set out to do, especially Buford. Candace tags along because Jeremy is on a trip to Paris, and she fears that there he may meet other girls. Also, Isabella finds her affections for Phineas sorely tested when his steadfast focus on achieving his goal puts pressure on her. Meanwhile, Dr. Doofenshmirtz takes a father trip to Tokyo, Japan with Vanessa, but sets out with Perry and Major Monogram to find her when she joins Phineas, Ferb and the others.
Phineas and Ferb build the ultimate lemonade stand and begin to offer franchise opportunities. Meanwhile, Candace and Stacy’s relationship is put to the test when Candace feels she must pick between their friendship and busting her brothers, while Dr. Doofenshmirtz creates a “Paper-Cut-Inator” so that he can make millions selling band-aids.
Khaka Peü Peü arrives in Danville to challenge Phineas and Ferb after the boys are mistaken as a superhero (while wearing an indestructible suit they designed to safely conquer their newly built extreme skate-track) known as The Beak. With the super villain wreaking havoc, it's up to Phineas and Ferb to thwart him while Dr. Doofenshmirtz tells the people of the Tri-State area that he is in charge, in hopes that they will actually just go along with it. Meanwhile, his brother Roger is worried that everyone will blame him for the recent super villain catastrophe so he decides to make Doofenshmirtz Mayor.
Irving’s brother Albert doesn’t believe that Phineas and Ferb are anything special, and since he claims to be the “Truth Detector,” he can prove it. Desperate to prove Albert wrong, Irving convinces Baljeet and Buford to pose as Phineas and Ferb beside a giant hologram of the boys’ Eiffel Tower construction. Meanwhile, Dr. Doofenshmirtz is fed up with the quality of accessories for his model train set, and decides to shrink down a variety of national monuments to add to his collection.
When the boys build an Anti-Gravity Fun Launcher, Carl accidentally intercepts their plans and assumes they are working for Dr. Doofenshmirtz, so he is sent undercover to figure out what they are doing. Meanwhile, Perry tries to find a lost agent, and Dr. Doofenshmirtz also acquires the blueprints to help with a parking issue on his street.
Candace panics when she inadvertently agrees to babysit Jeremy's little sister Suzy but to her surprise, Suzy is docile in the absence of her brother, saying that when Jeremy isn't around, she's "off the clock." The two of them bond and Suzy shows Candace how to get Phineas and Ferb to bust themselves. Meanwhile, the boys build a replica of Niagara Falls in their backyard with the intention of riding over the falls in a barrel. Back at Doofenshmirtz Evil Inc., Dr. Doofenshmirtz decides to increase his carbon footprint, (though he doesn't know what that is), by inventing a Carbon Footprint-inator.
Lawrence's memory is accidentally erased by a gadget in Perry's lair before participating in a father-daughter race with Candace, so Perry operates a robot version of Lawrence to fill in for him. Meanwhile, Dr. Doofenshmirtz invents an opposite of glue named "Eulg," which breaks stuff apart rather than join it together.
While Phineas and Ferb get the bubble ready, Isabella and the Fireside Girls head out to the "Old Abandoned Old Abandoned Amusement Park" where the maracanut tree is and try to get the sap from it. Meanwhile, Isabella's pet dog, Pinky tries to stop his nemesis, Professor Poofenplotz, from stealing hairspray.
The boys are able to create a giant bubble which enables them and their friends to float and view all of Danville from above as Candace tries to bust them while on a practice drive with Mom for her learner's permit. Meanwhile, Dr. Doofenshmirtz tries to gain popularity by singing country and western music and Perry must stop him before the concert crowd submits to his latest invention.
The boys travel into the future to borrow a tool, but when their future sister Candace finds what they are up to, she realizes that she has the evidence she needs to travel back into the past to bust her brothers. When she returns to her own time, she realizes that she has made a terrible mistake that only she can fix.
Stacy has a spa day planned for herself and Candace, but they get side tracked when Jeremy is participating in a house-building program for the homeless and Candace joins as well in hopes of impressing him. Fortunately, the girls are able to get their spa day after all when Phineas and Ferb build their own spa with its own special features. Meanwhile, Doofenshmritz finds a cat which causes a lot of problems when he's trying to carry out his latest evil plot.
When Candace finds a rabbit, she wants him as her pet, but in hindsight, he's actually a rouge agent trying to find Perry's secret lair for information. Meanwhile, Phineas and Ferb try to make x-ray glasses. And since Perry isn't around to stop his latest plot, Doofenshirtmz faces an unusual new foe.
Vanessa Doofenshirtmz tries to convince her dad that she's responsible enough to have her own car. For that, she has to get a special chemical for him in hopes she doesn't always have to ride with him on the family scooter. At the mega mall, a chase for the chemical ensues as it's tossed around between Candace and Stacy, Buford and Baljeet, and Ferb, who joins Vanessa's quest in hopes he'll be able to get her attention.
Phineas and Ferb learn that Baljeet has signed up for rock camp and worries he may get his first failing grade. So the boys help by forming a band to help him express his feelings, especially for math. Meanwhile, Candace wonders why Jeremy doesn't give her a cool nickname as Stacy gets close to Coltrane, the rock camp director. Doofenshmirtz's latest plan has him wanting his own army of babies by broadcasting his heartbeat all over the tristate area.
Phineas and Ferb build a ocean liner so that Baljeet can go on a romantic cruise with his friend Mishti, whom he now notices is a very pretty girl. Meanwhile, Doofenshmirtz wants to move all the lighthouses to the other side of town so that he can get a good night's sleep instead of hearing the constant noice from the boats surrounding the bay by his headquarters
The family takes a short sail trip out to sea, but a storm causes them to wind up stranded on a remote island. To pass the time, Phineas, Ferb, and Isabella, build a set of treehouses with the most modern conveniences, to Candace's dismay, as she wants to get back home in time to attend Jeremy's party. Meanwhile, Perry the Platypus, who was left behind, must get away from the watchful eye of Baljeet and Buford, so he can go on his mission to stop Dr. Doofenshmirtz's latest plot.
Phineas and Ferb set out to build a bigger plane than Howard Hughes' wooden Spruce Goose, so they build it out of papier-mâché, to do a similar theme to the Spruce Goose, complete with in-flight service and entertainment. Dr. Doofenshmirtz is doing his part to be green by using recycled materials to build an "Evaporator-inator" to dry up all the pools in the Tri-State area. Meanwhile, Candace and Stacy attend Jeremy's pool party only to discover an adventurous Australian girl is capturing Jeremy's attention.
It's another average, logic defying day for Phineas and Ferb, until a crashed space pod, carrying an unbearably cute alien, Meap, thrusts the boys into another adventure in space! Everyone has a different role to play, while Candace holds on to Meap by accident, Ferb is fixing up the ship, as Phineas uses the new cute tracker to find where their new friend is, to the slight irritation of Isabella, as he can't get what *cough* is causing cute interference, but of course, it all has to lead up to the big explosive finale in SPACE -ace-ace. Meanwhile, Doofenshmirtz has a new plan, simplistic in nature, but buried in an avalanche of backstory, oh dears.
Buford has a new game, "Jump and Duck", which everyone is loving the look of. But Phineas is always one for a challenge, and Candace's comment about a game "sucking them in" is just the inspiration he needs to create a virtual reality machine of "Jump and Duck". The trouble begins when Candace, in her preparations for a Cotillion Jeremy has asked her to, gets pulled in before the boys. Meanwhile, Doofenshmirtz has a slightly more disturbing childhood horror revenge story, but is the song and dance really necessary for this one?
When an early end to their daily project causes Phineas and Ferb to mistake an egg for Perry's, the boys use all their technological knowhow to help hatch the new part of the family. However Candace has different plans for the egg, as a nature show brings her to be the one to convince Phineas and Ferb that the newborn will need a real mother. Meanwhile, Doofenshmirtz is doing all he can to convince Perry that his latest scheme really is evil.
While in London, Candace and Stacy decide to take a page out of Sherlock Holmes'…entire collection, to figure out what Phineas and Ferb have planned for the London Eye. Meanwhile, Perry must team up with British agent 00 Zero in order to stop Dr. Doofenshmirtz from moving Big Ben to the Tri-State Area.
Curious as to what Perry's chirping sound really means, Phineas and Ferb create a "Perry Translator". But they soon find it's not just bound to translating platypuses, platypi, platypeople? Meanwhile, Perry himself is caught in a plan involving a shark cage that is half off, a remote to open the dam, complicated acronyms and the high tech BO-AT.