Classic Reality:
The Classic Reality. This reality is based on the world of The Alien Wars 1 - The Alien Wars 3. The original trilogy took place in a reality based off the Mega Man X reality, but had advanced many, many decades beyond that. The year is 2240 during the summer months of the year. There are many races and aliens in the universe, including many that are found in the Prime Reality - such as the Tsivrixsh Empire, which have been the enemeies in The Alien Wars and The Alien Wars 2: The Galactic Conflict.
The last of the X games that are in canon with this reality is Mega Man X4, in which Repliforce went Maverick. Following that, the next hundred years so many changes for Earth, including Reploid slavery and supression. Now, in the present day, after a minor Maverick War led by Death Star, in which reploids were shown to have souls by Slasher, Reploid and Humans have entered a new era of peace. The Hunters are located in a space station around Earth, their goal is to protect Earth from outside forces and threats on Earth too big for any organization to handle. On Earth itself is the Special Unit, a military police unit that investigates crimes and threats around the world.
Following the ressurection of many of their past enemies once the ex-President Wind brought everyone back to life, the 5th Column under Senreich, an ex-Nazi, brought the Nazis back to power and formed the Fourth Reich, taking over the Earth and plummeting the planet back into a dark age when the heroes emerged out of a time portal into a hellish world that they had to win back.
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Alternate Reality:
The Alternate Reality followed the same path as the Prime Reality up to a certain point. When the Prime versions of our heroes went back in time to stop Xevil at Centerpoint, they created a branch off reality. Essentially, by going back in time and preventing him from corrupting the Multiverse, they changed everything. In order to compensate for the change, the Alternate Reality followed the new path set by the heroes - Xevil did not create the multiverse, instead it was created by Cheryl and the heroes based on their memories. The Prime Reality retained the old timeline, though it was now attached to this new Multiverse. The Prime Heroes left and the Alternate Heroes were cut off from the Centerpoint Reality Core and had to escape, only to watch Centerpoint be destroyed all on it's own - somehow knowing Xevil was dead, they returned to their own lives.
The Alternate Reality thus was forever changed by that incident. The battle with Xevil on Centerpoint did not occur as it had before. They still fought Wind and defeated him, and Erevis still saved Megumi Zhenmei and became close to her - only this time as sisters due to Xanatos Durran no longer dying due to Prime Cheryl destroying the Planet Killer to give him a chance at a happiness in this reality. In the end, Cheryl did all this so that Ben would have a mother and father and a chance at life, since Prime Ben had died. She vowed, though, if things ever turned bad for Alternate Ben, she would take him away to the Prime Reality.
So, from there, the Alternate Heroes faced many challenges that were not the same as before - they spent the following year having fun, only to return to Earth to find it had been taken over by the Dark One shapeshifters; they defeated them and the Gift of the Gods was triggered earlier, with Katrina wishing Chii a soul. Xanatos and Erevis moved in with Darien Starr and became closer. The Weapons began to attack sooner than they had before due to some unknown enemy out there, since they never ran into Alexander Cran as they had before. Wtih no Legion, things began to play out different.
Today, the universe has been plunged into a hellish nightmare under a newly discovered race from the Gamma Quadrant called the Illium after the Light Device connected the two galaxies and allowed them in and the leader of the Illiums married Ao, leader of the PAX Empire. From there, the galaxy had fallen under the control of them since the PAX Empire ruled the entire galaxy in this universe. Pocket resistances fight against the Illium to rescue their captured friends and family for the past 5 years, trying to turn the tide against the seemingly unbeatable Illium armada.