Genesis Wave

The Genesis Wave is a phenomenon from the crossover Worlds Collide that is created by using the energies of a Chaos Emerald to rewrite reality. The technology to perform the Genesis Wave was originally developed by Doctor Eggman as part of his "Operation: Clean Sweep". While the Genesis Wave can drastically alter reality from a world(s), often leaving the affected inhabitants with amnesia or senses of deja vu, the wave has limitations as explained by Eggman and Wily: for one thing, it is apparently incapable of outright erasing individuals from existence.

Sonic: Genesis
By using the blue Chaos Emerald in his Death Egg, Eggman planned to alter reality in his favor. With the press of a button, a flash of light makes the world fade, changing everything. In the new world, Sonic the Hedgehog and the Freedom Fighters were inexperienced, never entering into a battle before. However, they were still able to defeat Eggman. As time passed, several earthquakes happened on the planet, the reality having been damaged by the Genesis Wave. Sonic, Sally, and Eggman recovered part of their memories from the original reality, and while Sonic faced Eggman in the Death Egg, the dimension started to tear apart. By using chaos energy, Sonic became Super Sonic and used Chaos Control to return things back to normal before their world is gone, Sonic returned 10 seconds before the Genesis Wave was activated, giving him time to save Sally from a turret that had hit her.

However, Eggman had prepared a second stage to Operation: Clean Sweep in case the first didn't work. By altering reality, he undid the immunity against roboticization set by the Bem, and he had a giant roboticizer installed in his Death Egg to roboticize everyone in the planet. Regardless of the roboticization working or not, if someone attempted to roboticize something that's already mechanical, it would explode. Therefore, Eggman would be the only person with technology available, destroying all machines from his enemies, and although it would destroy his forces outside of the Death Egg as well, if the roboticizer worked, he would have millions of robot slaves to serve as replacements. Sonic and Sally managed to destroy his roboticizer, but at the cost of Sally being roboticized. Eggman ordered Mecha Sally to throw Sonic out of the Death Egg. Later, Eggman was informed that the blue Chaos Emerald used in the Genesis Wave disappeared, and that the Death Egg was damaged and low on power, forcing Eggman to retreat.

Worlds Collide
Later, in another dimension, Dr. Wily was talking with Ra Moon in the Lanfront Ruins. Wily was interrupted by Flash Man, who reported that he found a large gem in the forest. The blue gem was the Chaos Emerald that disappeared in Eggman's world, being apparently transported to Earth after the Genesis Wave. While attempting to analyze the gem, Wily accidentally hijacked a communication with Eggman, and the two doctors formed an alliance. By using chaos energy, the doctors created a dimension for themselves, which they named Skull Egg Zone. They would then create the Wily Egg in the zone and start a second Genesis Wave from it during Mega Man #24 and Sonic the Hedgehog #247 (FCBD 2013), altering their worlds. The Skull Egg Zone allowed the doctors to keep the memories from their original worlds. After the changes, they started collecting the Chaos Emeralds for their main plan.

Super Genesis Wave
By using all seven Chaos Emeralds, Eggman and Wily planned to start a "Super Genesis Wave", allowing them to completely reshape their worlds without limitations. While they succeeded, Sonic and Mega Man entered a super form before the wave started, allowing them to stay and fight against the doctors' Egg-Wily Machine X. After the battle, Super Sonic and Super Armor Mega Man used Chaos Control to restore their worlds, with Sonic coaching Mega Man on how to do so. Mega Man successfully restored his world and bid farewell to Sonic. However, Sonic was interrupted by Eggman while attempting to restore their world, resulting in Mobius being broken apart, and thus resulting in Sonic and his allies trying to find the Chaos Emeralds to undo the damage.