When Isabella falls prey to hiccups, Phineas and Ferb gather the kids together to help scare them out of her, using a remote controlled haunted house. Meanwhile, Doofenshmirtz sets out to destroy his mentor's hideout, so that no one could discover his secrets, but not if Perry has something to say about it!
The boys build a rocket ship to get a good look at a star named for them, and Candace accidentally takes a ride with them just as she is trying to find the courage to ask Jeremy to a dance, while Isabella tries her best to do the same with Phineas. Meanwhile, Perry must stop Dr. Doofenshmirtz, who, not only is conveniently in space too, but has created a massive spacestation in an attempt to get revenge on "Huge-Hands-Hans".
Major Monogram and Dr. Doofenshmirtz host this special episode counting down the top 10 most popular music videos from the show's first season as voted by the fans and viewers, but not without the evil doctor attempting to pull off another scheme to gain power. Fortunately, Perry the Platypus is there to save the day.
Phineas and Ferb travel to the future to find a tool that hasn't been invented yet, and run into future Candace. Seeing an opportunity to finally bust her brothers, she follows them back through time to catch them building their rollercoaster, and exposes their antics to her mom. In the process, she accidentally foils Agent P's defeat of Dr. Doofenshmirtz, starting a chain reaction that turns the future into a dystopian society.
Phineas and Ferb try to decorate the Tri-State Area as a thank you for Santa Claus, but when Dr. Doofenshmirtz tries to spread naughtiness across the city with his "Naughty-inator," the boys must help restore holiday cheer to Danville. Meanwhile, Candace tries to find out the contents of Jeremy's wish list.
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.
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.
Isabella is upset the rain has ruined her chance of getting a Fireside Girl patch, so the boys create a huge biodome in the yard to help her; Candace's obsession with Jeremy is harming her friendship with Stacy, so she plans a day with her. However, Doof zaps her and Jeremy with the Combine-inator, and they can't go anywhere apart.
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. 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."
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.
The boys make a giant inflatable wading pool for Mom. Candace reveals her "Emo" side. Doofenshmirtz attempts to become ruler of all bees. / Isabella and the Fireside Girls turn themselves into bees. Poofenplotz tries to become Queen of the World by stealing and consuming massive amounts of royal jelly.
Spider-Man, Iron Man, Thor and Hulk stand powerless after being struck by Dr. Doofenshmirtz's power-draining "inator." Once the supervillains – Red Skull, Whiplash, Venom and M.O.D.O.K. – find out that Dr. Doofenshmirtz is responsible for robbing the superheroes of their powers, they seek him out and together create mayhem in Danville. Meanwhile, Phineas and Ferb do everything they can to restore the superheroes' powers before the evil villains take over the world.
After facing the choice of imprisonment or community service, Doof becomes a teacher at Vanessa's school. Meanwhile, a trio of bugs embark on a journey to become the first insects to communicate with humans. / Perry helps Doof in retrieving his father's old lawn gnome. Meanwhile, Phineas and Ferb help out their father on Father's Day
Isabella unintentionally admits her feelings for Phineas in a letter. Meanwhile, Doof invents an inator to help change his misfortune / 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.
It's been 10 years after the events of the present, and Phineas must decide what university to go to. After discovering that Isabella had a crush on him for years, Phineas must reach her before she leaves for college and express his true feelings for her. Meanwhile, Doofenshmirtz has a mid-life crisis.
Dr. Doofenshmirtz and Major Monogram have their hearts set on revealing the top 10 musical numbers from Seasons 2 and 3, but soon find out that celebrity host Kelly Osbourne has been brought in to fill the role. Unwilling to submit to playing second fiddle, Doofenshmirtz makes it his mission to thwart Kelly until Perry the Platypus sets out to stop his nemesis from ruining the entire show. Maia Mitchell ("Teen Beach Movie") also guest stars.