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.

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).

In the midst of a violent invasion of Earth by unknown alien forces, photojournalist Wakatsuki Tetsuya comes across a scantily-clad alien woman, cutting a swath of death through the Terran ranks with her sword. After a chaotic struggle, Tetsuya is knocked unconscious, only to awaken aboard her starship. To his surprise, she turns out to be Kahm, the invaders' princess - and she has picked Tetsuya for a starring role in her upcoming wedding. As the groom...

A promotional preview summary of the events in Detective Conan Movie 09: Strategy Above the Depths. Aired before the movie.