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.

When Charlie (Aaron Stone) discovers that his father worked for the Omega Defiance, the news sends him into a tailspin as he tries to prove that his father wasn’t evil. Charlie follows clues left by his father to track down an intelligence serum, which leads Aaron to a rematch with Damaged over the vial. With new threats to the world, T. Abner Hall enlists Vas and Ram to create a "Hero Rising" expansion pack incorporating the new villains to help Charlie train for his inevitable confrontation with this new evil. Meanwhile, Jason pretends to be Charlie as he begins working at the video game and comic store.

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

Aaron is photographed while stopping an armored car heist, forcing him to let Mr. Galapagos escape when more cameras are present. Meanwhile, Jason, and a classmate who has a crush on him begin to question just who and what S.T.A.N. really is.

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.

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.

A bad guy called 'Powers' abducted Emma, so Aaron has to find her and get her back. For his bad Powers has a satellite system built to chase and destroy Aaron Stone.

Aaron and Dark Tamara have to go undercover at a private school to find out what's going on with some students and to see if Damaged is involved.

Damaged hires a high-tech bounty hunter named Trace to hunt down Aaron Stone. Meanwhile, Charlie manages to catch the eye of the track coach by using his special shoes, the X5's in the long jump, much to Emma's chagrin since he is only supposed to use those shoes on Aaron Stone missions.

Charlie's plans a date with a girl named Carrie watching her favorite horror movie. But his plans are thwarted when Hybrot, Damaged's liquid computer that can steal and store memories sneaks into the house. Charlie must find a way to shut down the Hybrot, get his friends' memories back, all without revealing his alter ego to Carrie and Jason.

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.

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 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.