The Doomsday Project's prototype model was first deployed against the Wolf Pack. Sonic the Hedgehog, Sally and Antoine joined their canine allies in disabling the pod, though they were nearly defeated and captured by Snively.
As part of his final plan for the Project, Robotnik erected an enormous tower to deploy thousands of pods across Mobius by opening subterranean tunnels. Combining forces, all the Freedom Fighters launched an assault on the tower. However, they proved unable to destroy the machine until Sonic and Sally utilized the energies of the Deep Power Stones. The tower was then destroyed, seemingly taking Dr. Robotnik with it (although two ships were seen escaping, one could have been the Freedom Fighters and the other implied to be Robotnik's ship).
After this, Snively's pod which he used to survive opens up, revealing the villain, now dressed in a purple cape and black gloves. Pleased that his uncle finally let Sonic defeat him, Snively plans to take Robotnik's place. The worst part is that he was not alone.