Hooboy.
In late 1994, Xavier’s son David (going by the name “Legion”) went back in time 20 years and attempted to kill Magneto. A younger Xavier intervened and, oops, got killed instead. This happened in a very destructive and televised battle that Apocalypse happened to be monitoring, which convinced him that the time of mutants was at hand and led him to attack humanity much, much sooner. This happened around X-Men #41, I believe. The X-Men’s Bishop had followed Legion into the past, and was the sole survivor. And he bumped his head, so he couldn’t remember a darn thing.
So Marvel had fun by temporarily cancelling and replacing ALL the X-Men titles. The following week, we were treated to X-Men: Alpha, which replaced “our” universe. Basically, Apocalypse had conquered North America and killed most of the normal humans living there. He was opposed only by Magneto’s X-Men, which consisted of…lemme see…Rogue, Sabretooth, Blink, Iceman, Storm, Banshee, Nightcrawler and a few others. Magneto found Bishop, learned that the world was screwed up, and hatched a plan to fix history. It spread into the following titles:
Astonishing X-Men: chronicled Rogue’s team and their battle against Apocalypse’s son, Holocaust.
Weapon X: the adventures of Wolverine, who had one hand and was dating Jean Grey.
Factor X: chronicled Mister Sinister and his evil forces: the Beast, Cyclops, Havok, and a bunch of others.
Amazing X-Men: another team of X-Men. Kinda boring.
Generation Next: Bunch of young mutants. Colossus goes looking for his sister, the only time-traveler left.
X-Caliber: Nightcrawler and Mystique go looking for Destiny in the Savage Land. The Juggernaut has a neat death scene.
Gambit and the X-Ternals: Magneto sends Gambit after the M’Kraan crystal.
X-Man: Cable clone. The only AOA title to continue into the modern Marvel universe.
X-Men Chronicles: gives snippets of the Age of Apocalypse history; and…
X-Universe: tells the final fates of Tony Stark, Don Blake, Gwen Stacy, Matt Murdock, Victor von Doom and a bunch of other heroes in this universe.
The whole thing wrapped up in X-Men: Omega. I remember spending hordes of money on these books, which just goes to show you that George Lucas isn’t the only person with a brilliant marketing scheme. There’s paperbacks, but they’re hard to find now.