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The Commander and Jetstream are two superheroes, but who also live a suburban lifestyle and work as real estate agents under the names Steve and Josie Stronghold. Their son, Will, tries to live up to the family name, but has yet to reveal any powers.

In the airborne high school, "Sky High", Will fails the Power Placement test, and is assigned to be a "Sidekick". At the end of his first day at high school, the Commander entrusts him with the 'key' to the family's Secret Sanctum (after promising that he will never bring anyone else there); the place where all the family's trophies of past victories are kept, including a strange device called the "Pacifier". The Commander tells Will about how the Pacifier was taken from an arch-enemy supervillain named Royal Pain, but little else is mentioned of Royal Pain's demise or the Pacifier's powers. Will had intended to confess that he is just a "Sidekick", but as his dad is daydreaming of Will growing up to fight crime beside his parents, Will doesn't have the heart to tell him the truth. Both of them are unaware that a mysterious eavesdropper is spying on them via the eye of a giant robot that Will's parents defeated earlier.

Will manages to cope through his school experience, spending all his time with his fellow sidekicks, and his best friend Layla, however, they suffer bullying from the students classified as "Hero" - Will in particular is hazed by the pyrokinetic Warren Peace, the son of supervillain Baron Battle (whom the Commander sent to prison). Layla has the mysterious ability to manipulate plants; but as she refused to show it in Power Placement, she has also been ranked as a sidekick. Will finally reveals to his father that he is only a sidekick and admits that he has no superpowers, but his father still maintains the belief that he will yet turn out to be a great superhero.

The next day, Will is tripped into Warren by school bullies Lash and Speed, leading to a fight in the cafeteria and, when his friends are threatened, Will accidentally discovers he has superhuman strength. As a result, he is re-classified as a "Hero" and made to leave Sidekick Class and his friends. Will becomes friends with the gorgeous Gwen Grayson - who has the power to control machines with her mind - and their relationship is mistaken for love by Layla. Unknown to Will, Layla secretly fancies him and, after Will forgets to go to a restaurant with Layla because Gwen comes to the Stronghold house for dinner, Layla pretends to be dating Warren to get back at Will.

Gwen convinces Will to let her planning committee for the school homecoming dance meet at his house while his parents are on a mission. However, Gwen actually invites almost every Hero from Sky High and it becomes a house party. Gwen seduces Will to let her into the Secret Sanctum (in order to be alone while they kiss) - Speed sneaks in at the same time and steals the Pacifier.

Layla comes in to see what's going on and Gwen takes the opportunity to convince her that Will no longer likes her or any of the other Sidekicks. Disgusted at Gwen for driving away his best friend, Will dumps her and ends the party - just as his parents get home. Will tells his parents that he won't go to homecoming and tries, unsuccessfully, to get in touch with Layla. He runs into Warren, who informs him that Layla isn't dating him and actually loves Will.

The Commander and Jetstream head to the homecoming without Will. While putting away his dad's old yearbook, Will notices that a girl named Sue Tenny, who went to school at the same time as his parents, looks just like Gwen and is holding what looks like a prototype Pacifier in one of the photos. Realising that the Pacifier has been stolen, Will heads to Sky High with the aid of Ron Wilson, Bus Driver.

At the school, Gwen shocks everybody by revealing she is Royal Pain and uses the Pacifier to turn everyone, except Warren, Layla, Zack, Ethan and Magenta who escape down a vent, into infants. Zack's seemingly useless power to glow proves itself by allowing the gang to see where they're going. Will arrives at the school, and meets up with his friends, who begin to tell him about Royal Pain. He reconciles completely with Layla even kissing her, then takes on Royal Pain alone. She reveals that she is in fact Sue Tenny - she was believed to have no powers the first time she attended Sky High (as her power wasn't officially recognised at the time) and vowed to take revenge by turning everyone there into babies and raising them again as supervillains. During her first battle with Will's parents the exploding Pacifier actually turned her into a baby and she was brought up again by her sidekick Stitches as Gwen Grayson. Will is flung though a window, but discovers he can also fly and defeats Royal Pain.

Will's friends take on the bullies. Lash is defeated by Ethan, Speed is defeated by the combined forces of Warren and Ethan and Layla easily defeats Penny once Penny makes her mad enough to fight back by slapping her. Stitches tries to get away with the babies but is stopped by Ron Wilson. Penny reveals that Royal Pain sabotaged the anti-gravity device that keeps the school airborne and the sidekicks convince Magenta to use her ability to become a guinea pig to climb down a pipe and deactivate Royal Pain's device.

The defeated Royal Pain triggers the sabotaged anti-gravity device, causing Sky High to fall. Will flies out of the window and prevents the school from touching down while Magenta quickly works to repair the device. The device is repaired, and the school returns into the sky. The infants are all returned to their adult state by reversal of the Pacifier's powers, and Royal Pain and her minions are given time to cool off in the detention room. After they show the graduation dance then they show Will and Layla kissing floating. A comic-book like sequence at the end, narrated by Will, shows that Gwen and her gang are now in prison, Ron Wilson (who, like Will, had superhero parents but no powers) now possesses superpowers and works as a superhero and that Will and Layla are dating and Warren is Will's new best friend