The colour scheme of the heroes and villains (red, blue, white, black, green, brown) was not continued in the Hero Factory theme, instead, colours like silver, gold, orange, and yellow were reintroduced. The direct Recon Team story was discontinued after the HRT service was shut down, though it remains an element in the main story. After the incident with Von Ness, Stormer is determined that no rookie would ever put a mission in jeopardy again and is especially harsh on them as a result; many prior rookies under his command either gave up or were transferred out. Like his fellow rookie teammates, he was built with experimental designs, but resented the constant examination this required.

The Alpha 1 Team attempts to intervene, but is soundly defeated, necessitating a risky upgrade into stronger forms to help combat the new threat. Voltix then uses the black hole staff to cause a villain breakout, leading the Heroes to conclude that Von Nebula wanted the staff to be placed inside Hero Factory for a grander scheme. The exception is the Von Nebula and Rotor sets which have 156 and 145 pieces respectively and are packaged in a larger box of the China. The first four TV episodes aired continuously over four nights in September 2010, and were later released onto DVD as a singular film titled Hero Factory: Rise of the Rookies on November 16.Here, Heroes are built in the Hero Factory and sent on missions around the universe, dealing with a variety of galactic problems such as alien infestations, natural disasters, and criminals. Those with less than 40 pieces are the cheapest toys in the range, though there are figures and sets with up to 450 pieces to be built. He has been actively working to develop his intelligence, increasing his amount of reading and vocabulary. From 2011 onward the characters were modeled with four-fingered fists instead of the 2009/2010 three-fingered fists. During the 2013 storyline, the Heroes have to fend off an invading army of native creatures controlled by the Brains, a species of parasitic organism dispatched by a mysterious villain.

He employed some former jailbird henchman who banded together to help him, but that was unknown to the heroes. As with BIONICLE, there were six main heroes released per line (this tradition did not continue with the Breakout waves and beyond). A check as to whether these reviews come from users who have actually used or bought the product in question has not been carried out unless the user review appears alongside the label 'Verified Review'. He later learns that his body has been corrupted by nanobots from the sludge and, after a fight with Stringer, Bulk and Furno, escapes the Hero Factory.

Stormer gives permission to Furno to come down and states that his mission trial is to chain up Rotor. Rocka is told of the situation by Zib before Black Phantom deactivates all the Mission Managers with his mysterious Anti-Quaza. The third wave of Hero Factory sets was released in mid-2011, further expanding the new building system. The main characters are a group of heroes that make up Team Alpha 1, the Hero Factory's most successful and praised team.