An evil force unleashes alien brains on Makuhero City; the alien brains have the power to turn nice guys into bad guys.

There is a jailbreak at the maximum security prison of Hero Factory! Criminals like the crazed Toxic Reapa, the evil Jawblade and the schizophrenic Splitface have broken free and are spreading chaos and destruction all across the galaxy! It is revealed that the villainous Black Phantom is behind the prison break, and that it was merely a distraction for the heroes, so he could attempt to destroy Hero Factory's Assembly Tower while they were recapturing the escapees. Evo, Surge and Furno are sent on missions to catch and cuff the villains, while Rocka remains at Hero Factory to stop Black Phantom, who already has the mission managers neutralized, and destroy his Arachnix pet.

There is a jailbreak at the maximum security prison of Hero Factory! Criminals like the crazed Toxic Reapa, the evil Jawblade and the schizophrenic Splitface have broken free and are spreading chaos and destruction all across the galaxy! It is revealed that the villainous Black Phantom is behind the prison break, and that it was merely a distraction for the heroes, so he could attempt to destroy Hero Factory's Assembly Tower while they were recapturing the escapees. Evo, Surge and Furno are sent on missions to catch and cuff the villains, while Rocka remains at Hero Factory to stop Black Phantom, who already has the mission managers neutralized, and destroy his Arachnix pet.

While Sir Makuro reveals the latest line of upgraded Heroes, a group of power-hungry villains attack Fueling Station 22. It is up to the Alpha Team to clear the site, but their outdated bodies are no match for the powerful villains and their leader, the Fire Lord.

When Rocka goes missing after responding to a civilian's distress signal, Stormer, Furno, Nex, Bulk and Stringer are sent to find him.

When Rocka goes missing after responding to a civilian's distress signal, Stormer, Furno, Nex, Bulk and Stringer are sent to find him.

When a construction site is attacked by XPlode and Rotor, the Alpha Team is dispatched to deal with the situation. Rookie William Furno decides to join in, only to mess things up. This motivates him to train harder.

Three Heroes are caught up in a futile fight against the acid-spewing Corroder, and their only hope is to form a shield, using their energy reserves. But their Hero Cores are nearing depletion, so William Furno decides to jump into action and save his friends.

The evil Meltdown sprays Preston Stormer with a substance that causes him to go insane and threaten his teammates. After he breaks out of the confinements of the Hero Factory, William Furno has to find his leader and save him from himself.

A mysterious black hole opens up above New Stellac City, and the Heroes go to investigate. Upon arrival, not only do almost all the villains show up they've met so far, but their worst enemy, Von Nebula also looms over them.

A new Rookie team has been assigned to complete their training with Stormer and his crew. Furno looks to be the best Rookie the Factory has seen since Stormer was a Rookie himself. He takes his position as a Hero in training very seriously and yearns for Stormer’s approval, and will push himself to do whatever it takes to get it. He’s joined by fellow Rookies Breez and Surge, as they try to prove to Stormer and each other why they are ready to become true Heroes. As the six Heroes begin to work together on their missions, they start to realize that the bad guys they are fighting are working for someone. Someone from Stormer’s past, with an evil agenda to take down the Hero Factory and Stormer himself.