Remember when Marvel sent most of its big-name heroes to Battleworld, having them disappear from their own books for one month? It was a little thing called Secret Wars. People like to dump on Jim Shooter, but with that event, he led Marvel forward into a storytelling model that is still being used today.
Age of Apocalypse took Secret wars to the next level. It involved every single X-title, but rather than have the mutants disappear from their own comics, Marvel stopped publishing all of the X-line and replaced it with alternate reality versions of the regular series. For example, Generation X became Generation Next. X-Factor became Factor X. And so on. Just like the Clone Saga did for Spider-Man, AoA completely cancelled all of the X-family of titles (X-Men, Uncanny X-Men, etc.), replaced them with new books, and then cancelled all those new books and returned to the pre-AoA publication slate (with a few minor revisions).
None of these titles are in the Earth 616 narrative timeline, which takes them out of my blog. For my purposes, they are not canon.
The basic story: In Legion Quest, Charles Xavier sacrifices himself to save Magneto. Because of that, Magneto sees the good in the world and takes on Charles’ mission. Apocalypse is then able to take over the world.
All the books that emerge in this timeline flow from that. It’s basically just a four-month extended “What If?” story. It was good, it’s just not 616 canon so I’m not covering it. Similar to how I handled the (godawful) Spider-Clone event and series, I’m just noting their existence in this post and moving on to other things.
It ended in X-Men: Omega #1 (1995), when Bishop went back in time to the event that created the timeline–Legion killing Xavier–and manages to kill Legion before he can kill the Professor. With that the “normal” 616 timeline “unfreezes” and the regular X-books resume publication.