The team eventually forces Jack to face the fact that he's not really putting his heart into their training. Dylan keeps trying to escape, Tucker has self-esteem problems and trouble controlling his powers, and the kids are annoyed by Jack's attitude. At first, things do not go well, with Jack being bitter about the past, and his sarcastic attitude disappoints Marsha.

The project holds an audition of would-be members, and four 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. 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. He is also told that if natural training does not prepare the new team in time, they will be exposed to Gamma-13. He is told that a new team is needed to battle a great menace but is not told what it is. Jack finds himself dragged back into the Project, this time as an instructor. General Larraby, the military officer in charge of the Project, decides to form a new Zenith Team to fight him.

Ed Grant, the scientist behind the original Zenith Project, discovers that Concussion is making his way back into their dimension. Robby Benson was believed to have been destroyed by Freddie Benson at the cost of his powers, but was sent into another dimension instead. Thinking Zoom and the team betrayed him, Robby Benson killed his teammates Brad, Raeven Chase and Wes. This made Zoom faster and stronger, but it also turned Concussion evil. The American military sought to enhance the team's powers using an experimental form of radiation called 'Gamma-13'. 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 ('Captain Zoom') and his older brother, Connor Shepard ('Concussion').

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