Headmasters starts with Galvatron leading a new batch of Decepticons to wage war on Cybertron, the Decepticon Headmasters. The Autobots are rescued by the arrival of the Autobot Headmasters, led by Fortress (Cerebros, the head of Fortress Maximus). It is revealed that Fortress 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 Autobots/Decepticons war.

The Autobots' Supreme Commander, Star Saber, defends the Earth against the forces of Deszaras, the Decepticons' new Emperor of Destruction. Deszaras desires the planet's energy to reactivate his massive planet-destroying fortress, sealed away in the Dark Nebula long ago by Star Saber.