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.

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.

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.