Welcome to the Age of Apocalypse Fan Site
The crew had been through the ringer in the prior years. Starting with the Phoenix Saga, Jean Grey had been overtaken by the Phoenix entity and seemingly died as a sacrifice for the others. Then word from the future warned of a dystopian timeline where mutants were hunted to near extinction by the Sentinels. Then the underground Morlocks were attacked, a Mutant Registration Act was enacted, and interdimensional demons arrived with the curiously familiar Madelyn Prior.
Offshoots, X-Factor and X-Force both had their involvement when Cable and Stryfe took center stage, nearly crippling the X-Teams. This led to Magneto and his Acolytes attacking from Asteroid M, leaving Wolverine without his adamantium skeleton, and Colossus turning to the dark side. A final blow came when the Phalanx arrived and began to infect the crew with a techno-virus, ultimately leading to the death of fan-favorite, Blink, and the formation of the newest young X-Men: Generation X.
But all changed when Professor X's insane son, Legion, decided that Magneto needed to be snuffed from the timeline at a point before he caused any damage. Traveling back to the 1970s, his goal was to kill Magneto and avoid all the trouble that occurred after.
Now Professor X and Magneto were actually good friends at this point, neither adhering to any strong ideology. Four X-Men--Bishop, Iceman, Psylocke, and Storm--were able to hop along Legion's time travel, although all lost their memories upon their destination. Slowly each regained their purpose, and Legion eventually found Magneto. However, instead of killing him, Professor X jumped in the way and instantly wiped out the current timeline, removing Legion and most of the X-Men from reality. Only Bishop remained, as he was an interloper from the future and was able to exist outside the timeline.
Apocalypse, who had been alive for centuries, witnessed the act via broadcast and decided to initiate his plan for world dominance early. Magneto would attempt to follow the more noble path that Professor X had forged, but it was too later, and the world fell into disarray.
Thus began a several month saga beginning an ending with X-Men Alpha & Omega, with the current x-titles rebranding in the mean time. The changes were as follows:
Uncanny X-Men -- Astonishing X-Men
The read order was meant to follow the publication dates, but since the conclusion, some issues filled in the backstories. Generally, start with the two X-Men Chronicles, X-Men Alpha, then all the first issues of the monthly comics through the forth. Conclude with X-Men Omega and X-Men Prime.
All the details over the course can get a bit messy, so I recommend reading the FAQ to get a good overview. Check out the great one by Marty Blaze:
So that wraps up the main points. Key issues of AoA also came with foil and prismatic covers, which were big at the time, giving them a fantastic look and a price to match. I made sure that I ordered each via catalog as them came out, but the mall had the missing issues handy when that took a too long (6-8 week delivery was the norm at the time).
I managed to score a free poster though from one of my orders:
So what happened after Age of Apocalypse?
Well, it was mostly retconned back to the status quo. Most everyone died in the ensuing battle within the alternate timeline, sacrificing themselves to restore the original. I lost track after that, and mainly followed Generation X, and the 2099 series, but I believe the evil version of Beast managed to escape into the correct timeline, and was doing something with the techno-virus again.
In 2005, ten years later, a series popped up that revealed that the AoA timeline was actually kept intact, despite healing the main universe. Those who were left, had to pick up the pieces and manage what was left.