Following the Battle of Autobot City, the mortally wounded Optimus Prime passes on the Matrix of Leadership to Ultra Magnus. As the new host of the Matrix, Magnus is targetted by Unicron, who sends Galvatron and the Decepticons to kill him and destroy the Matrix. Magnus and his team of Autobots are chased from Earth across the stars, finally being cornered on the scrap-metal planetoid, Junk. Most of the Autobots take cover under a mountain of junk while Magnus faces the Decepticons alone. He tries to open the Matrix - which is said to "light the darkest hour" of the Autobots - but it will not open for him. Galvatron orders his Sweeps to open fire on Ultra Magnus and the Autobot leader is struck down by a swath of laser fire. Magnus collapses dead and his body explodes into pieces, and Galvatron takes the Matrix for himself.
Later on, when Hot Rod, Kup and the Dinobots arrive on Junk in a stolen Quintesson ship, they make peace with the planet's Junkion inhabitants. The Junkions offer their friendship to the Autobots and salvage Ultra Magnus' body parts, putting him back together and restoring him to life.