Scourge managed to find Cybertron during the Great Shutdown, an enforced shutdown of all Transformers on the planet, and managed to reactivate Shockwave for the purpose of observing the Decepticon from afar. However, Shockwave was soon attacked by the Quintesson Sharkticon extermination units left behind on this world. Forced to intervene, Scourge easily destroyed a number of Sharkticons and drove off the rest, saving Shockwave's life. As a way a saying thank you, Shockwave shot Scourge in the back, took him prisoner, dissected him and studied the Unicronian Transformer, gaining great knowledge of Cybertron's origin and its inhabitants.
Scourge (or another drone like him) escaped to Earth and attacked Jetfire and Omega Supreme's shuttle just as it arrived on its mission to search for the missing Ark. Tricking the drone into pursuing an escape pod, Jetfire managed to shutdown the advanced Transformer's systems and was dragging him back to their crashed ship when they were both buried in an avalanche.
Thousands of years later, the Autobots were drawn to the Alaskan shore, right into a trap set by the Decepticons. The Autobots fought desperately to keep the Autobot escape pod out of Megatron's hands, and during the fighting, it was inadvertently activated. Just as the Autobots gained the upper hand, Scourge ordered the combatants to stand down, informing them that the war was over, the factionalism that had divided their race had ended, and Cybertron was now unified under a new leader. Before he could speak further, Shockwave shot him in the back, declaring both Autobots and Decepticons to be war criminals.