Some time before the event, on Sonic's homeworld of Mobius, the evil Dr. Eggman had acquired a Chaos Emerald in order to power his new Death Egg Mk. II. Equipped with an outlandish reality-warping weapon known as the Cosmic Reset, Eggman attempted to reshape Mobius in his own image, but his tampering with time and space was undone by Sonic the Hedgehog who tapped the power of the Chaos Emeralds and transformed into Super Sonic, using Chaos Control to reverse Eggman's Genesis Wave, setting the world right again. However, the Chaos Control wave not only restored Mobius to its proper state but had the unforeseen effect of warping the Chaos Emerald housed in the Death Egg's power core away. The emerald's location would not be discovered for some time...
On Earth in the year 20XX, in a region known as the Lanfront Ruins, Dr. Albert W. Wily had discovered a strange alien construct known as Ra Moon. This entity was a supercomputer capable of analyzing and replicating any technological data in order to produce new robots and Dr. Wily used the device to create a new legion of Robot Masters as well as resurrect his previous line which had been destroyed by Mega Man. As Wily established his new base of operations in Lanfront, his forces discovered a mysterious blue gemstone that seemed to contain an awesome power of alien origin. Wily attempted to analyze the gem's properties with the aid of Ra Moon when, to his surprise, he recieved a signal from an unknown source that was being channeled through the jewel. This signal turned out to be a communication from Dr. Eggman who was attempting to trace the Chaos Emerald's location across space.
Doctors Eggman and Wily communicated with one another and discovered that they had much in common: both were master robotic scientists and engineers, they had similar plans for their respective worlds, and both men were constantly being thwarted by blue-coloured heroic nuisances. With Eggman's guidance, Wily used the power of the Chaos Emerald to create the Skull Egg Zone, a pocket dimension linking both their worlds together. By combining resources, the two doctors shaped the realm to their liking and created a flying battle fortress from which to enact their schemes for all reality: the Wily Egg. After using the Emerald to launch a second Genesis Wave, the pair set out to acquire the remaining Emeralds. In order to accomplish this, they captured a number of Sonic the Hedgehog's allies and transformed them into the evil Roboticized Masters.
The Main Event
Quickly securing most of the Emeralds, the doctors then arranged for their foes - Sonic and Mega Man - to be tricked into battling each other in the hopes that one or both would be destroyed. The battle began on Mobius, but soon moved to Earth as Mega Man's creator and Wily's rival, Dr. Light, created a Warp Ring to bring his robotic son back home. Fearing further interference, the doctors dispatched Metal Sonic and Bass to capture Light as Sonic and Mega Man continued to battle. However, the heroes eventually learned that they had been deceived, forcing the doctors to attack with Tails Man, the first of the Roboticized Masters. By combining their abilities, the two heroes unexpectedly returned Tails to normal, and learned of the doctors' alliance. Transporting to Light Labs, they would arrive too late to prevent Dr. Light's capture, but were able to pursue him into the Skull Egg Zone accompanied by Proto Man and Rush. After a brief battle with Mega Man's old enemies Copybot and the Genesis Unit, the heroes ran into the full force of Roboticized Masters.
Proto Man left his allies in order to locate the missing Dr. Light, dividing the Roboticized Masters as several were called off to pursue him. By modifying Mega Man's Mega Buster weapon to mimic Sonic's Spin-Dash attack, the heroes succeeded in restoring all three members of the Chaotix to their normal forms. The detectives left to join Proto Man, while the doctors dispatched Robot Master Shadow Man and Roboticized Master Shadow Man to engage the heroes. Despite the formidable team, the heroes were victorious, restoring Shadow the Hedgehog and destroying Wily's Shadow Man. Thanks to Shadow's Chaos Control abilities, the heroes also became aware that reality had been altered, and became even more determined to set things right. Silver Man and Blaze Woman were likewise turned back into Silver the Hedgehog and Blaze the Cat by the heroes, while the doctors began work on a deadly battle vehicle, the Egg-Wily Machine X. Unbeknownst to them, the Wily Egg had been boarded by Rouge the Bat, who made contact with Dr. Light for his help in sabotaging the flying fortress.
Sonic's team soon battled the last remaining Roboticized Masters, Knuckles Man and Rose Woman, who had been ordered to self-destruct in order to eliminate the heroes. Fortunately, after a heated battle, they were able to return them to their normal forms of Knuckles the Echidna and Amy Rose. Having succeeded in rescuing all of Sonic's allies - that they were aware of - the heroes set out to assemble them and regroup at the Wily Egg, which had stopped thanks to Rouge's sabotage. Unfortunately, Rouge was captured by the doctors and subjected to Roboticization, becoming Rouge Woman. She was then deployed alongside an army of Robot Masters the doctors had time-cloned from Earth's past against Sonic and Mega Man's force. Joined by E-123 Omega, the heroes put up a valiant fight despite being outnumbered, even succeeding in rescuing Rouge. Realizing that they were fighting a losing battle, however, Sonic and Mega Man departed for the Wily Egg with Tails and Rush, just in time to see Dr. Light jettisoned from the craft.
After Light was rescued by Shadow and joined the allied heroes, Sonic and Mega Man boarded the Wily Egg to confront Eggman and Wily. The evil doctors, their friendship shattered by Eggman's attempt to murder Dr. Light, dispatched the Mega Man Killers to impede their progress. Following a swift battle, the Killers were destroyed, but Tails was injured and forced to retreat with Rush. Fighting their way up through various obstacles, the heroes encountered the Chaos Devil, a monstrous creation of the villainous doctors. Their battle with the creature came to a halt with the arrival of Duo, a powerful ally from Mega Man's universe, who sent the heroes ahead while staying behind to handle the creature. Mega Man and Sonic continued, but faced a final obstacle: Metal Sonic, Bass, and Treble, who tag-teamed the two heroes viciously. After a grueling battle, the two succeeded in defeating them, only to be captured by the Egg-Wily Machine X. Held captive by Eggman and Wily, the heroes then learned the full scope of the doctors' plan: to completely rewrite all of reality using the Genesis Reactor, a device powered by all seven Chaos Emeralds.
Outside the Wily Egg, the battle with the Robot Masters continued, and Sonic's allies were soon joined by an unexpected force of arrivals: the original Robot Masters created by Dr. Light. Taking advantage of the reprieve, Knuckles and Proto Man-joined by Rush and Dr. Light-boarded the Wily Egg to aid Mega Man and Sonic. The red heroes took on the doctors while Light and Rush freed Mega Man and Sonic, who then used the power of the Chaos Emeralds to transform into Super Mega Man and Super Sonic. The doctors also super-charged the Egg-Wily Machine X, leading to a titanic struggle between the blue heroes and their enemies. During the fighting, the Super Genesis Wave was unleashed, consuming all of reality in its blinding light as the heroes managed to defeat the doctors. Harnessing the power of the Emeralds for one final act, Sonic and Mega Man prepared to restore their worlds to normal. Mega Man succeeded without incident, but Dr. Eggman launched a final attack against Sonic, greatly disrupting his efforts.
The after-effects of the disrupted Genesis Wave were minimal on Mega Man's world. However, Sonic's world was drastically altered thanks to Dr. Eggman interrupting Super Sonic's Chaos Control; history was largely re-written, certain places and individuals were erased from the timeline whilst others were radically changed. The planet itself had suffered cataclysmic damage that left its continents fractured and divided, yet due to mysterious energies emanating from the planet's core, the continents remained within a gravitational field and did not scatter into space. Both the Freedom Fighters and the Eggman Empire are currently working towards restoring the planet from the brink of destruction, though they are not working together.