Genesis Wave

The Genesis Wave is a phenomenon created using the energies of a Chaos Emerald to rewrite reality to better fit the user's benefits. The technology was originally created by Dr. Eggman and was used to alter Mobius on three occasions. On the third occasion, it was reinvented by Iggy Koopa and used by Bowser Jr. to merge his world with Mobius. A supercharged variation made possible with the power of at least seven Emeralds is called the Super Genesis Wave.

Description
The Genesis Wave has the ability to rearrange the space and time of a dimension, allowing the user to create a new timeline, reshape the physical universe, rewrite memories, and alter the structure of universes. The time-space altering effects of the Genesis Wave will linger for a short while, creating disturbances that can be detected throughout the new reality's timeline, like when Sans registered the anomalies in the time-space continuum.

The Genesis Wave's capabilities are limited by how many Chaos Emeralds are used. With just one, the Genesis Wave can only tweak the timeline and bend the occasional rules of the world. It is also incapable of outright erasing individuals from existence. With all seven Chaos Emeralds, however, the user can release a supercharged version of the wave, known as a "Super Genesis Wave." This wave has no limitations to it and can completely reshape the world however the user deems fitting, including erasing others completely and turn beings into deities. The Genesis Wave also cannot completely erase old memories. A regular Genesis Wave for example often leaving the affected inhabitants with amnesia or senses of deja vu. The memories affected by a Super Genesis Wave also still exist, but cannot be accessed at all. Space-time disruptions from Chaos Control can also partially restore a person's old memories.

Despite its power, usage of the Genesis Wave has its dangers: overuse of it can greatly strain the fabric of reality, up to the point of literally "breaking" a universe. The Super Genesis Wave presents an even greater risk, capable of causing apocalyptic damage to the entire multiverse and all of existence itself if used incorrectly, or if it is improperly reversed. In addition, unlike the effects of a normal Genesis Wave, the Super Genesis Wave's effects are irreversible: once the affected world is changed, it presumably stays that way forever.

Sans seems to have a partial immunity to the effects of the Super Genesis Wave. As such, he can remember how timelines were before alteration.

Development
The Genesis Wave was conceived by Dr. Eggman during his recovery from insanity. Theorizing that Sonic was apparently the embodiment of chaos, thereby making him an unpredictable element that would spoil any of his plans, the doctor came up with the Genesis Wave to neutralize that factor. After escaping New Mobotropolis' prison, Eggman and Snively began developing the Genesis Wave.

First Wave: The Mecha Sally Saga
After completing and launching the Death Egg Mark 2 with the blue Chaos Emerald, he unleashed the wave as part of Operation: Clean Sweep. The resulting reality was different in a number of ways from how it had previously been. This included a timeline where Eggman and Snively could easily take over Mobius, and where Sonic, the Knothole Freedom Fighters-minus Bunnie-and Eggman had not met until the "new" present.[15] However, the changes the Genesis Wave had caused threatened to destroy the entire dimension. As Eggman failed to cement his grip on the new reality with his World Roboticizer, Super Sonic used Chaos Control to restore reality to its previous state. However, the effects of the Genesis Wave awoke the merged spirits inside Ixis Naugus, left half of Mobius' population vulnerable to roboticization (including Sally, who was roboticized herself) once more, and sent the blue Chaos Emerald to another dimension.

In the Underground, a Royal Scientist, Dr. Alphys, manage to regenerate the lost prince of the Underground as a flower.

Second Wave: the Chaos Emerald from Mario's world
When Dr. Albert W. Wily came into contact with Eggman after finding the blue Chaos Emerald, the two bonded and decided to work together to conquer their worlds, with the Genesis Wave being essential to their plan. Meeting up inside the Skull Egg Zone, the doctors constructed the Wily Egg with its own Genesis Wave machine. Within the zone, thereby allowing them to retain their memories of their original realities, the doctors launched the second Genesis Wave, which affected their respective worlds in different ways; while Mobius' timeline was completely reset (into a different state than last time), the timeline of Mega Man's World flashed into the future with only slight alterations. This also established a bridge between the worlds for the doctors to use. Unaware to the two doctors is that the green Chaos Emerald duplicated and arrived in Mario's world. Unaware of that, the two doctors gathered the seven Chaos Emeralds to super-charge the Genesis Wave for a "Super Genesis Wave" to alter the realities further, this time to completely reshape their worlds to their exact vision with no limitations and turn themselves into deities, despite the risk of heavily damaging the fabric of space and time in the process.

Meanwhile, in the Underground, an Overlander named Frisk fell.

Third Wave: Super Genesis Wave
The green Chaos Emerald duplicate was found by Bowser. After Kamek realizes that it can rewrite the whole universe, Bowser let his own version of "Operation: Clean Sweep" in the hands of his nephew, Iggy Koopa. Bowser Jr. took over the operation after learning about it, unaware about the plans Eggman and Wily had. Bowser Jr.'s plans were, practically, to stop Eggman's. Sonic and Mega Man were unable to prevent the Super Genesis Wave from being unleashed and rewrite both their universes, but they were still able to infiltrate the wave while in their super forms, in which they attempted to reverse with Chaos Control. Super Armor Mega Man was able to successfully restore his world, with everybody native to his world returning to their proper place. Super Sonic's attempt at restoring Mobius, on the other hand, was met with interference by Eggman. Bowser Jr.'s attempt to reset his world was as well met with interference from Mario. Because of the interferences, the Prime Zone's restoration was distorted. In order to prevent Sonic's Multiverse's collapsing, a god named "the Merger Magikoopa" asked for help from Sans Gaster. Sans managed to reshape the Prime Zone in such a way that the Chaos Emerald from Mario's world merged with Bowser Jr., turning him into a living Chaos Emerald, and the Prime Zone merged with the Underground. Although this made Bowser Jr.'s Genesis Wave successful, his enter in the Prime Zone led to the original timeline to restart from zero, albeit with some things (Sonic and Sally being secretly into a romance) left unchanged, to blend the Koopas in. It also failed to prevent the creation of another timeline based more on the games and vulnerable to demon attacks.

The effects of the Super Genesis Wave in the various Multiverses

 * The Prime Zone got split into multiple pocket zones, some of which vulnerable to demon attacks. One of them, the Neo Prime Zone, is controlled by the Merger Magikoopa.
 * Eggman and Robotnik Prime merged.
 * In some timelines, Shard the Metal Sonic and Metal Sonic v. 3.0 got merged as well.
 * Sonic and Sally's relationship was changed.
 * In some timelines, they are just friends.
 * To make matters worse, Sally became a lesbian.
 * In the Neo Prime Zone, they still are a couple, only that secretly.
 * Nicole's backstory was changed.
 * The Chaos Emerald from Mario's world merged with Bowser Jr., turning him into a living Chaos Emerald.
 * The Koopa Kingdom became part of the Prime Zone.
 * Bowser managed to create his Galactic Empire without any resistance.
 * It is unknown if he would have declared war on Mobius. Because he loves his son more than anything, it is unlikely.
 * Mario's fate became unknown. It is heavily implied that he never met Bowser Jr. in the Neo Prime Zone.
 * Sans's mother became his guardian angel.
 * Frisk started to try doing Pacifist Runs again, as their memories of the 4822 Genocide Runs started to haunt them.
 * Undyne became a Sonic fan without knowing it.
 * Because Mega Man met no resistance while undoing the Super Genesis Wave, his dimension got restored just the way it was before the Genesis Wave.

Trivia

 * Given that universes can be restored from the Genesis Wave by inducing Chaos Control, it would suggest that the Genesis Wave is simply a refined version of Chaos Control.
 * The Genesis Wave's name is likely a reference to the Sega Genesis game system, on which the Sonic the Hedgehog games debuted; indeed, its first usage altered Mobius's reality to make it more like the earliest Sonic games, while the effects of the second and Super Genesis Waves should have resulted in a world based even more on the games, only to be drove away from them by Sans.
 * The Genesis Wave is also synonymous with the infamous Genesis Device from the movie Star Trek II: The Wrath of Khan. The Genesis Device unleashed a terraforming wave that would alter a planet to be hospitable, almost similar to how the Genesis Wave would alter a reality to take a different form.
 * Thanks to his research, Sans knows about the power of the Genesis Wave, calling it as a reset.