Dark Awakening

Dark Awakening is an episode from season three of the Generation One continuity family.

On the run from Galvatron, the Autobots take refuge on board the mausoleum ship containing many of their deceased comrades. These include Ironhide, Prowl, Ratchet, Huffer, and Optimus Prime, who is strangely alive again thanks to a Quintesson plot. After Optimus saves their lives, Rodimus Prime eagerly returns the Matrix to him, despite his bizarre behavior and damaged appearance. After he re-assumes command, Optimus's dangerous, erratic behavior forces Hot Rod to reclaim the Matrix from his zombified mentor, who still possesses enough of his true heroic self to partially fight back against the Quintesson's reprogramming. When he does, the irreparable Optimus's last act is to pilot the mausoleum into a sun. And thus, the tears of untold thousands of young boys flowed all over again.

However, Prime's intact but still deceased body (perhaps a second one?) was apparently saved from the ship (also intact; possibly another one as well?) by Jessica Morgan and Gregory Swofford, leading to the events of The Return of Optimus Prime.