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.

While Sir Makuro reveals the latest line of upgraded Heroes, a group of power-hungry villains attack Fueling Station 22. It's up to the Alpha Team to clear the site, but their outdated bodies are no match for the powerful villains and their leader, the Fire Lord. Later, when Rocka goes missing after responding to a civilian's distress signal, Stormer, Furno, Nex, Bulk and Stringer are sent to find him.

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.

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

In the city of Antropolis, a drill for a new underground Metro Line project reveals strange creatures called Jumpers from within the planet that abduct the crew. Hero Factory send in Evo to investigate, which leads to an attack on the city by giant beasts. The Alpha 1 Team is flown in to stop the monsters by building battle machines to combat the beasts.