Phineas, Ferb, and their friends are surfing on an asteroid belt in outer space (“Surfin’ Asteroids”) while Agent P confronts Dr. Doofenshmirtz. Before Agent P destroys it, Doofenshmirtz’s “Power-Draininator” inadvertently fires a beam that bounces off the kids’ space station and hits Iron Man, Spider-Man, Hulk, and Thor, who are facing off against Red Skull, Whiplash, Venom, and M.O.D.O.K. in New York City (“My Streets”), rendering them powerless and allowing the villains to escape. On the S.H.I.E.L.D. helicarrier, Nick Fury notifies them that the beam came from Phineas and Ferb’s station, and they go to the boys’ house to confront them, but the two profess their innocence. Meanwhile, after finding out that Doofenshmirtz’s Power-Draininator has drained the heroes’ powers, the villains pay him a visit, initially thinking him to be an evil genius.Phineas and Ferb: Mission Marvel 2013.
After running less-than-evil errands with Doofenshmirtz, which include stomping on a bed of leaves and going up the down escalator (“My Evil Buddies and Me”), the villains realize Doofenshmirtz’s incompetence and decide to bring the heroes to them by attacking the Googolplex Mall.
Meanwhile, Phineas, Ferb, and their friends plan to assist the heroes in a self-built defense facility, aptly titled the “Secret Hideout for Emergency Defense” (or S.H.E.D. for short) which is much bigger on the inside. They build a machine to temporarily duplicate the lost powers, but due to Candace’s interference, the heroes’ powers get mixed up (Thor has Spider-Man’s powers, Spider-Man has Hulk’s powers, Iron Man has Thor’s powers and Hulk has Iron Man’s powers). The heroes and Phineas and Ferb, equipped with their Beak suit, go to the mall to face the villains, but are quickly subdued, and subsequently rescued by Agent P wearing a superhero costume. Back at the S.H.E.D., due to Candace interfering again, Baljeet is struck by a gamma ray from the power-replicating machine and turns into a Hulkified version of himself before storming off. Phineas lashes out at Candace and revokes her S.H.E.D. card while Buford goes out to look for Hulkjeet.