Ultra Magnus and the Autobots crash land on Junkion, where Galvatron catches up to Magnus and murders him, stealing the Autobot Matrix of Leadership for himself. He flies off to confront Unicron.
When Hot Rod and the other separated Autobots return from the Quintesson planet, the Junkions, led by Wreck-Gar, repair Ultra Magnus and reveal their planet of junk to be a giant spaceship. They head for Cybertron to combat Unicron.
Galvatron attempts to use the Matrix to make Unicron obey him, but the Matrix will not work for him. Unicron swallows Galvatron whole as he proceeds to attack Cybertron. The Decepticons attempt to fight back, but to no avail.
The spaceship piloted by Hot Rod and Kup flies right into Unicron’s eye, and Hot Rod confronts Galvatron from inside Unicron. They battle briefly, and as Galvatron attempts to crush Hot Rod by the neck, the Matrix begins to glow. Hot Rod takes a hold of it, and is changed into Rodimus Prime. Rodimus dispatches Galvatron, and then uses the Matrix to destroy Unicron. Rodimus tracks down the Autobots still inside of Unicron, and they escape out of Unicron’s other eye just before he is completely destroyed. Rodimus Prime then leads the Autobots to reclaim their homeworld, easily dealing with the diminished Decepticons, and leading Cybertron into a new age of peace.