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The Genesis Reactor is a device built by Dr. Eggman and Dr. Wily in order to launch their Super Genesis Wave and rewrite all of reality as they saw fit. Powered by all seven Chaos Emeralds, it had the potential to allow them total control of their alterations to reality, as opposed to the limitations of the waves previously generated by the Cosmic Reset Button using a single Emerald.
A Mad Plan
Having previously used the blue Chaos Emerald to rewrite the reality of both Mobius and Earth 20XX, Dr. Eggman and Dr. Wily devised an even more diabolical scheme: to use all seven Chaos Emeralds to totally reshape their universes. Successfully collecting all the gemstones, they plugged them into the Genesis Reactor, which continued to power up as they continued their battle with Mega Man, Sonic the Hedgehog, and their various allies. Rouge the Bat's sabotage of the Wily Egg, which carried the reactor, resulted in some of the building Chaos energy being lost, but the reactor quickly replenished itself. As it prepared to launch the Super Genesis Wave, the doctors revealed their plan to their captured nemeses. When Knuckles the Echidna and Proto Man attacked, the doctors drew some power from the reactor in order to supercharge their Egg-Wily Machine X. Dr. Light, upon examining the device, was unable to shut it down, but Sonic and Mega Man were able to reach the Emeralds and use their power to transform into Super Sonic and Super Mega Man. The reactor launched the Super Genesis Wave, which washed over the Skull Egg Zone and both universes, but its effects were undone by the two heroes, though Eggman managed to interfere in Super Sonic's efforts. (SU: #52, #53, #54, StH: #251)