Commander Rann returns to Homeworld from his 1,000 year exploratory voyage across the Microverse in his ship, the Endeavor. The evil Baron Karza has overthrown the ruling royal family with the support of the people. Rann escapes with Marionette, Bug, Acroyear, and Microtron.
After travelling through the Spacewall, the Micronauts land in a backyard in Florida, where they are only 6 inches tall. The encounter Steve Coffin, a teenage human and fight Battle Cruisers commanded by Shaitan.
The Micronauts defeat Shaitan’s battle cruisers. Biotron tries to repair the damaged Endeavor and rest of the Micronauts search for Bug.
On Homeworld, Karza’s troops round up the resistance. One of its leaders, Slug is sent to the Body Banks. On Earth, the Micronauts search for Bug while Ray and Steve Coffin take the remains of a Wing Fighter to Professor Prometheus at H.E.L.L.
On Earth, the Micronauts encounter the cyborg Professor Prometheus who has created a doorway to the Microverse with his Prometheus Pit. On Homeworld, Prince Argon has been altered into centaur form by Karza. The Baron chooses Slug as the host body for Duchess Belladonna.
The Micronauts escape from H.E.L.L. Ray Coffin meets Time Traveller. Argon and Slug escape the Body Banks. Karza views Professor Prometheus.