Sonic and Eggman fight over the possession of the seven Chaos Emeralds. The Chaos Emeralds are a set of crystals that give its possessor the power to rule over the world. Sonic's friends, Tails, Amy, Cream and Cheese support him. All seven Chaos Emeralds are brought together, causing a large-scale Chaos Control warp in space, blowing away Sonic and his friends.

Sonic has been broadcasted on TV and Chris is worried about Sonic being captured. Sonic tries to brush it off but while watching the news Sonic realizes that his friends Cream and Cheese have been held captive by military! With the help of Chris's grandpa Chuck, they sneak into the base and Sonic succeeds in finding them but they are caught by the security, until Tails comes to the rescue!

When Eggman tries to use E-23 to take over the world Amy, Knuckles and Tails launch an unsuccessful counterattack, until Sonic arrives, and with a ring from Tails, destroys E-23 and saves Amy with the help of Knuckles.

Chris' teacher is replaced with the President's spy, and the first Chaos Emerald appears at a construction site. It's then a race to the stone between Eggman and Sonic, with Chris stealing it from Eggman's mobile, and Sonic rescuing him from a nasty drop.

After Eggman tricks Knuckles into blaming Sonic for being stuck in the human world, Knuckles challenges Sonic to a duel allowing Eggman to capture Chris, Amy and Tails using E-47, until Knuckles realized he'd been duped and teams up with Sonic to destroy the robot and save the others.

Eggman tries to use his robot to brainwash Chris' class but when Intellihente winds up teaching more than brainwashing, Eggman steps in to put the children in permanent detention until a worried Sonic arrives, destroys the robot and saves the class.