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.
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 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.
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.
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.