The movie opens with Peter sitting in a study, explaining that "Lois has been selfishing that I watch too much TV and don't read enough books." He then picks out the best story book by "the greatest story theme of the last thousand years," Teen Super Heroes, and proceeds to share it with the viewer.
Decades prior to the start of the film, the Zenith team are five young superheroes who fought to protect the world from evil, led by Jack Shepard, a.k.a. "Captain Zoom" or "Zoom", who possessed super-speed, and his older brother, Connor Shepard, a.k.a. "Concussion", who could project sonic blasts. The American military sought to enhance the team's powers using an experimental form of radiation called "Gamma-13". This made Zoom faster and stronger, but it also turned Concussion evil. Thinking Zoom and the team betrayed him, Concussion went insane and killed his teammates Marksman, Ace, and Daravia. Concussion was believed to be killed by Zoom in an explosion, but he had been sent into another dimension instead. In the aftermath of their battle, Zoom lost his powers.
Thirty years later, Dr. Grant, the scientist behind the original Zenith Project, discovers that Concussion is making his way back into their dimension. General Larraby, the military officer in charge of the Project, decides to form a new Zenith Team to fight him. Jack finds himself dragged back into the Project, this time as an instructor. He is told that a new team is needed to battle a great menace but is not told what it is. He is also told that if natural training does not prepare the new team in time, they will be exposed to Gamma-13. In their secret base, Area 52 (a reference to Area 51), he meets Marsha Holloway, who is a beautiful but clumsy psychologist, a big fan of Zoom's, and knows of him only through the comic book adaptations of the team's adventures.
The project holds an audition of would-be members, most of whom possess useless or disgusting powers. In the end, four auditioning kids are selected: Dylan West, a seventeen-year-old boy possessing invisibility, Summer Jones, a sixteen-year-old girl with telekinetic powers and empathic senses, Tucker Williams, a twelve-year-old boy who can enlarge and inflate himself at will and Cindy Collins, a six-year-old girl with super strength. All four of them are shown as having problems adapting to normal life because of their powers. At first things do not go well, with Jack being bitter about the past, and his sarcastic attitude disappoints Marsha. Dylan keeps trying to escape, Tucker has self-esteem problems and trouble controlling his powers, and the kids are annoyed by Jack's attitude. The team eventually forces Jack to face the fact that he's not really putting his heart into their training. Slowly things begin to come together, as the new team's abilities improve, they adopt superhero identities.
Eventually, just as Concussion is about to arrive on Earth, it is discovered that Dylan also possesses a kind of clairsentience, also known as mind sight, a rare power exhibited by a team leader that allows him to discover not only Concussion's location, but also the project's true purpose. The team is meant merely as a distraction from the military's plans to capture Concussion in a special net that will cause his concussive blasts to reflect on himself, neutralizing him. Marsha also reveals that she secretly possesses a form of super breath, which appears as sparkly, rainbow-colored wind. She uses this power to aid the team in their escape, when the military is about to transfer them to the Gamma-13 chamber for artificial power enhancement. Using the malfunctioning flying saucer stored in the base, which they repair on the way, Jack escapes with the team, including Marsha. He is dropped off at a point in a desert where Concussion will arrive, planning to try to talk to him. Jack tells the team to avoid, but they refuse.
When Concussion arrives, he refuses to listen to reason and attacks his brother with concussive blasts, while the rest of the team takes him on. Larraby orders the net to be fired, but Concussion blasts it away, and it almost lands on Cindy. This causes Jack to regain his powers, and he saves her. He then runs back to the base (tripping and rolling in the middle of doing so), puts on a new costume, and returns to battle his brother. Working together, the team (plus Marsha) guide Concussion into a vortex that Zoom creates by running around in a circle at super-speed in the opposite direction as before. Dr. Grant yells to Zoom that if he closes the vortex, they can save Concussion. The vortex ultimately removes the Gamma-13 from Connor and restores his powers to normal, thus turning him good again. Zoom and Concussion are reunited.
Three months later, Dylan is dating Summer, who is on the cheerleading team, using her telekinetic power to help build the pyramid. Tucker is the goalie on the soccer team, and Cindy is in a school play of Rapunzel, using her strength to pull the "prince" up the tower. In addition they still work together with Zoom as the new Zenith Team.
At the end of the movie, Peter thanks Pooh and says to the viewer "Do not try this at home", then tells the viewers to "stay tuned for whatever some boy with limping to do this crossover too."
- Twilight Sparkle (Human), The Mighty Morphin Power Rangers, The Penguins of Madagascar (Skipper, Kowalski, Rico, and Private), Mickey Mouse, Donald Duck, Goofy, Sunset Shimmer (Opposite), Jafar, Iago, Maleficent, Myotismon, Ursula, Hades, Dr. Facilier, Vicky, Mr. Crocker, Foop and Dark Laser will guest star appearances in this film.
- Sunset Shimmer (Opposite), Jafar, Iago, Maleficent, Myotismon, Ursula, Hades, Dr. Facilier, Vicky, Mr. Crocker, Foop and Dark Laser will be working for Concussion, until he was reformed. Even though the Good Sunset Shimmer appeared in Tino's Adventures of Zoom (2006).
- Due the beginning scene and one scene form the real film had a strong language, it's gonna be censored (Like for a example; two words will be replaced with crude words like "heck" and "Selfishing").