The main characters are a group of heroes that make up Team Alpha 1, the Hero Factory's most successful and praised team.

Rocka is told of the situation by Zib before Black Phantom deactivates all the Mission Managers with his mysterious Anti-Quaza. A skilled strategist and problem solver, Zib has a no-nonsense attitude while working and will emphasises mission protocols with Heroes both on mission and in the Control Room. Two of the sets, Breez and Thornraxx, received a limited release in Europe, with a wider release as an addition to the summer line in the United States and elsewhere. Mark Surge is one of Team Alpha 1's youngest, a temperamental hot-head working to overcome a secret insecurity.The Alpha 1 Team attempts to intervene, but is soundly defeated, necessitating a risky upgrade into stronger forms to help combat the new threat. The LEGO Club magazine also introduced two combiners, an unnamed Hero, which is made of three Hero sets, and an unnamed Villain, which is made of three Villains the Heroes were after. Hero Factory is an animated TV series based on the Lego toy series of the same name and produced by Threshold Animation Studios for The Lego Group and Geely.

Bulk is always ready for a mission, and enjoys fighting for the Hero Factory as much as he enjoys the actual fighting itself. A facet of the Hero Factory storyline is the Hero Recon Team, based around a web application that allows users to design products using LEGO's Design byME service.

The villains have special parasite heads, holding parasite brains which have many similarities to the Krana and Kraata from BIONICLE. Surrounded, Breez talks to the Queen and convinces her to free the other Heroes and let them all leave.

Sent out on a dangerous mission to save a refueling station, the heroes are attacked by vicious Fire Villains, who prove too fast and too strong. All the villain sets have an age rating of 7–16 and are around 17 cm (7") tall besides Von Nebula who is around 22 cm (9") tall and has an age rating of 9–16 and Rotor who is around 20 cm (8") and has an age rating of 8–16. Voltix seems to be the ‘breaker-outer’ of the villains, since he was the one who allowed Von Nebula to break himself out of his own black hole staff, creating a black hole and allowing the villains to escape. Each Hero is unique, with their own distinct personalities and equipment, and the Heroes are arranged into teams.

The largest building and trademark of the city was the Assembly Tower, a 589 meters high, 715 meters wide and 924 meters long tower, located in the center of Makuhero City. Bulk's artificial intelligence is less developed than others, which he sometimes feels self-conscious about, but he makes up for this intelligence deficiency with sheer power.

In most cases, instructions for the models are found in the respective instruction booklets of the characters, with some exceptions. Some LEGO® sets contain small parts that are NOT suitable for, and may pose a hazard to, children under 3 years of age. However, the accidental death of one of the monsters causes the Queen to turn on the Heroes, forcing them to attack her.While all of the heroes are distracted by the escapes, Black Phantom stays behind to destroy the Hero Factory assembly tower.