Will Stronghold (Michael Angarano) is beginning his freshman year at Sky High, a high school which teaches super powered children. Will's parents are The Commander (Kurt Russell) and Jetstream (Kelly Preston), the world's most famous superheroes. Will's best friend is Layla (Danielle Panabaker), who has the power to manipulate plant life.
Will is anxious about attending Sky High, located on a floating campus reached by flying school bus, because, unbeknownst to his parents, he has not developed any super powers. The first day he and the other freshman are harassed by a trio of bullies: the super fast Speed (Will Harris), Lash (Jake Sandvig) who can stretch his body, and cheerleader Penny (Malika and Khadijah Haqq) who can create duplicates of herself.
Because of his lack of powers, Will is slated to enter a curriculum for “Hero Support” and become a sidekick. His classmates include Ethan (Dee Jay Daniels) who can melt into a puddle, Zach (Nicholas Braun) who glows in the dark, Magenta (Kelly Vitz) who turns into a purple guinea pig, and Layla who joins the class in protest against the two track nature of the school's education. The class is taught by The Commander's former sidekick “All American Boy” (Dave Foley).
The Commander, unaware that his son has been relegated to Hero Support, shows Will his secret trophy room. He is particularly proud of the mysterious weapon “The Pacifier” which he took from his science themes arch-nemesis Royal Pain years ago. Unknown to either of them, Royal Pain, who had been presumed dead, watches the exchange from a hidden camera in one of the other trophies. As Will settles in to Sky High and makes friends with the other sidekicks he comes into conflict with fire wielding student Warren Peace (Steven Strait), whose supervillain father had been imprisoned by The Commander. During a fight between the two, Will demonstrates super strength, impressing Gwen Grayson (Mary Elizabeth Winstead), a beautiful and popular “technopath” who controls machines with her mind. Will begins spending more time with Gwen and her popular friends, ignoring the sidekicks and Layla, who reveals to Warren that she has loved Will for a long time.
On the day before the dance, Gwen tricks Will into throwing a party at his house, and Speed steals the Pacifier when she seduces Will into showing her the Secret Sanctum. After Gwen is cruel to Layla, who shows up to investigate the noise, Will breaks up with Gwen refusing to attend the dance even though his parents are going as honored guests. Later, he looks through his father's old yearbooks and sees a student who looks just like Gwen. Believing that the student is Royal Pain and that Gwen is her daughter he rushes to the dance.
At the dance party, Gwen reveals that she is in fact Royal Pain. During her previous confrontation with the Commander, the Pacifier, which is meant to turn its target into an infant, had malfunctioned, turning her into a baby instead. She has since waited sixteen years for revenge. With the help of Speed, Lash, and Penny, she takes over the school and uses the Pacifier to turn the faculty and students into infants.
When Will arrives at school, he apologizes to Layla and teams up with Warren and the sidekicks to try and save the day. The sidekicks demonstrate their heroism after Royal Pain sabotages the school's anti-gravity drive and their powers come in handy restarting it. Will, meanwhile, discovers that he also has his mother's powers of flight when he is thrown off the edge of the school grounds and must prevent the campus from falling. Gwen and her henchmen are defeated and arrested and the faculty and students are returned to their proper ages. Will and Layla kiss and a voiceover at the end reveals that they become boyfriend and girlfriend.
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