Supplanting The Rebirth's position in Japanese continuity, The Headmasters occurred one year after The Return of Optimus Prime, introducing the title characters to the Transformers universe in a different way.

Six years after the decisive battle against Unicron, a group of rebellious Headmasters led by Weirdwolf join with Galvatron's Decepticons in an attack on Cybertron.

The situation soon gets worse when it is revealed that Vector Sigma, the super-computer at the planet's heart, is destabilizing, and Optimus Prime again sacrifices his life to save Cybertron.

Meanwhile, Scorponok replaces Galvatron- who had vanished in the explosion- as Decepticon leader, constructing a personal Transtector and redubbing himself MegaZarak to battle Cerebros' own giant form, Fortress Maximus.

Human Daniel Witwicky and his young Autobot friend Wheelie also played major roles in the series, serving as the youthful characters for the audience to identify with.

The dub is, however, infamous for its poor quality, full of mistranslations and incorrect names (for example, Cybertron is pronounced "Cyberton", Blaster becomes known as "Billy", Blurr is "Wally", Jazz is "Marshall", Hot Rod is "Rodimus" (pronounced "Roadimus"), the Matrix becomes the "Power Pack", Spike is "Sparkle", Soundblaster is "New Soundwave", Metroplex is called "Philip", and Fortress Maximus is occasionally called "Spaceship Bruce"), as well as stilted and even bizarre dialogue, such as "I'll send you express to hell!"

A novel based on this anime titled Transformers: The Headmasters - Dream War (トランスフォーマー ザ・ヘッドマスターズ 夢戦争, Toransufōmā: Za Heddomasutāzu - Yume Sensō) was written by Keisuke Fujikawa and released on August 25, 1987.