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.
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 It is up to the Alpha Team to clear the site, but their outdated bodies are no match for the powerful villains and their leader, the Fire Lord.
A rookie Hero named Rocka lands on jungle planet Quatros, where he discovers that the insane Witch Doctor has enslaved the local wildlife and is using them to mine the planet empty of quaza, threatening the entire planet's very existence.
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 ...