Short episodes streamed on the anime's official site after every episode, giving background information about the show.

Headmasters starts with Galvatron leading a new batch of Destrons to wage war on Cybertron, the Destron Headmasters. The Cybertrons are rescued by the arrival of the Cybertron Headmasters, led by Fortress (Cerebros, the head of Fortress Maximus). It is revealed that Fortress Maximus left Cybertron millions of years ago in search of energy, and have finally managed to come home. He explains that the Headmasters are from a planet called Master; the human-sized robots who live there built themselves Transformers-sized bodies. They can then transform themselves into the heads of the robots, and have now joined the Cybertron-Destron war.

The planet Libertia was once known as “the planet of death”, until humanity built three giant mirrors and created what seemed like an ideal land. It is on this planet that Professor Grace and his granddaughter Alcia live peacefully… until their home is attacked by Guild soldiers looking for the professor and for Legaciam – a special Armor that can resist extreme heat, allowing it to go to areas where humans would not survive normally. Alcia, who was at the time piloting Legaciam in order to help her grandfather with the testing, manages to get away… barely. But the Guild is determined to get Legaciam by any means necessary…

Even though the Decepticons have been driven off Earth, a small team of Autobot Pretenders have remained behind, just in case. Led by Metalhawk ("Hawk" in his human identity), the Pretenders live among the humans, using their Pretender shells to assume human size and appearance. The Autobots' caution is rewarded: Decepticon Pretenders soon appear, led by a mysterious force called Devil Z. The Autobots and Decepticons soon build up their forces, recruiting humans to become Junior Headmasters and Godmasters (Powermasters).