Charlie loses his first Hero Rising ever to a new player named Grudge, a teenage boy trained by Elias Powers. Grudge is working with Damaged to take down Aaron Stone and unleash a deadly virus on the world, and when Damaged, U and Elias Powers capture the President of the United States, Aaron Stone must infiltrate the White House, free the president and stop the mutants before it's too late.

Charlie is forced to ditch his date with cheerleader Irina Webber when a new and improved Mr. Galapagos returns to steal the Forced Fusion battery. Meanwhile, Jason invites a bunch of girls from school to go on a joy ride in Charlie's new car.

Aaron is detained for questioning when he seemingly kidnaps T. Abner Hall and must convince S.T.A.N. and Dark Tamara that it wasn't him, but the shape-shifting mutant U.

A new threat arises when the evil hooded villain, Damaged, frees himself and a bus full of failed experiments, criminals and mutants. Once free, Damaged begins picking off the remaining Omega Defiance members looking for the last vial of intelligence serum. Dr. Necros comes looking to Aaron Stone for protection, but instead lures him into Damaged’s clutches. Meanwhile, Jason is determined to get Charlie a dream job working at the video game and comic store.

Charlie takes his brother Jason to the 'Hero Rising' tournament for his birthday with Vas, Ram, Emma and Stan in tow. At the tournament, the Omega Defiance locates Aaron Stone and sets out to destroy him. Jason sees Charlie as Aaron Stone for the first time battling it out against the Omega Defiance, but thinks it's a show Charlie's put on for his birthday.

A second Stan shows up because of Kronis' wormhole and Charlie must find and stop Kronis before people start noticing there are two Stans.

Charlie is saved from Helix's hybrids, leaving Stan behind. Will Charlie disobey direct orders from Hall to go back and save him?

Aaron Stone has to stop Cerebella, whose video is hypnotizing millions of kids.

Xero, the evil boy computer genius, takes over a high-tech skyscraper and challenges Aaron to fight his way out through a gauntlet of modern office equipment that has turned deadly.

An experimental toxin is spilled all over Charlie during a mission. The toxin causes Charlie to have spells where he acts more and more aggressive. Emma teams up with Vas and Ram to retrieve the antidote.

Aaron Stone enlists Dark Tamara for help when Zefrin and his ninjas steal a weather device from Hall's secret storage facility to destroy a metropolitan city. Meanwhile, Jason takes a photo that threatens the secret identities of Charlie and S.T.A.N.

When Charlie borrows the SSJ to go to a party in India with Vas and Ram Stan unexpectedly joins him. The two are knocked out of the air by the mutant-loving geneticist Helix and stranded on his island.

Even though Aaron's gut instincts about one of Hall's scientists being shady is dismissed by Hall, Aaron is validated when the scientist offers him a chance to steal from Hall.

Charlie realises that Emma has never been to a school dance before and decides to take Emma to their school formal and invite Vas and Ram as their guests. Charlie picks them up in the SSJ, but on the way, Hall sends Aaron Stone on a mission to pick up a set of blueprints before Kronis gets to them. When, Kronis captures and holds Vas and Ram hostage, he will only release them in exchange for the blueprints. Aaron Stone must enlist Hall's daughter, Tatianna, to find Kronis, save Vas and Ram and make it to the dance before it's over.

Aaron Stone (Charlie) is injected with a chip that allows Tranq to enter his dreams and uncover Aaron's ultimate weakness - fear that harm will come to his family. Now S.T.A.N. must find a way to remove the chip before Tranq takes over Aaron Stone's mind.

While trying to stop Sector 21 escapee Hive from turning the world into mindless zombies, Aaron Stone unknowingly transports African Zombie Weevil bugs containing Hive's mind controlling venom back to Eastland. The weevils hitch a ride on S.T.A.N. and end up infecting Jason and half of the school. With the toxic venom slowly transforming them into insects, Aaron must get a sample of Hive's venom to Emma so she can engineer an antidote before it's too late.

Xero kidnaps the world's most feared fighter, World Champion Billy "The Body Bag" Cobb, to teach them the moves necessary to program his combat suit. Aaron Stone is enlisted to rescue Billy Cobb and destroy the combat suit.

Stan is replaced by Hunter, a hip teenage android who helps Aaron Stone battle General Cross, but Aaron completly forgets about S.T.A.N in place of the new Hunter. During a fight, Hunter takes a blast from a laser pistol on the mission and ends up short circuiting, causing him to think that his new mission is to destroy Aaron Stone.

Charlie develops a crush on Tatianna Caine, a girl he rescues while trying to recover stolen radioactive material. After Tatianna reveals a secret about herself, S.T.A.N. must rescue Aaron. Meanwhile, Emma enlists Jason to help run her campaign for class president.

When Jason accidentally sells the Gauntlet, Aaron must confront Shackles without his trusty weapon. Meanwhile, a criminal uses the Gauntlet to rob a bank.