Oh yeah, it’s my time to shine:

Basically, there are these things in the comics called Genesis Waves, created by Eggman and his nephew, Snivley, after they broke out of prison sometime in the comics. The machine is powered by a single Chaos Emerald (which, in the comics, they for some reason are as powerful as MCU Infinity Stones) and when it sends out a Genesis Wave on Eggman’s command, the wave is essentially able to REWRITE THE DIMENSION for a short while. It also rewrites other dimensions adjacent to it. The limits of the wave are that it can only tweak the timeline, bend the occasional rules of the universe, and it cannot erase people from existence. Also, memories can be rewritten, but the individuals who’s memories were rewritten still experience deja vu and occasional flashes of memories. HOWEVER, it’s capabilities are only limited by how many Chaos Emeralds are used, in which, if all 7 are used, the user becomes an omnipotent being, and can completely reshape the entire dimension and its multiverse as they see fit. They have no limits. They can erase people from existence, turn beings into deities, etc.

The first Genesis Wave, Operation: Clean Sweep, was launched by Eggman on the Death Egg MKII, where Sonic and Sally were trying to stop it, but Sonic got preoccupied with Silver Sonic. Sally decided to go ahead and find and beat the shit out of Eggman, but then she got fucking obliterated by a hidden double-barrel turret. Right as Sonic realized she just literally died, Eggman launched the wave and rewrote reality. Sonic then found himself running in Green Hill Zone, thinking he just spaced out for a second, and then he went and saved some animals from the rewritten Snivley, which happened to be the Freedom Fighters, although none of them remember who the other one is. After going through all of Sonic 1 and Sonic 2’s zones, Sonic regained his memories in the Death Egg, absorbed Chaos Emerald energy from a power cable, which was hooked up to the Death Egg, which was powered by the Chaos Emeralds, allowing him to turn into Super Sonic, defeat Eggman, and then use Chaos Control to fix reality back to normal (Chaos Control is buffed af in the comics).

The Super Genesis wave, created by Eggman and Dr. Wily from Mega Man’s world (yes, this is canon), was launched while Sonic and Mega Man were in the final fight in the Wily Egg. They might have been unable to stop the wave from launching and their universes being permanently messed up, but they were still able to infiltrate the wave itself while in their Super Forms (Mega Man also has a super form here) and beat the doctors. At the end, they just stare into their fucked up Universes as Mega Man’s just like “uhhhh so what now?” Sonic then is like “oh yeah lmao let’s just use Chaos Control,” and Mega Man’s like “what the fuck is that my guy? Is it legit that easy to fix the whole fucking universe?” Sonic then teaches him how to use Chaos Control, and then Mega Man fires a Chaos Control Megabuster at the void and then his universe is fixed, albeit he retained none of his memories from the entire arc and the Mega Man X timeline was created as a result of that. Sonic, on the other hand, while he was charging his Chaos Control, Eggman fucked up his concentration by ramming into him, and even though his Chaos Control was fucked, Sonic’s just like “well, here goes nothing,” and throws it into the void. Then, the entire void just shatters and it all fades to white. What happened there is that Sonic’s entire dimension got completely fucked up. The entire main universe had its timeline completely rewritten, Mobius was now just simply Earth, the version that’s most accurate to the games, all of the other universes got completely reset, and the wave just happened to be too much for Earth to handle, so it just started breaking apart, leading to Sonic Unleashed, or the Shattered World Crisis.

Then, later on, because of the Super Genesis Wave, Genesis Portals were created, which can lead to other universes, and Sigma, the main antagonist of Mega Man X, was able to manipulate those portals, leading into Sonic and Mega Man: Worlds Unite.