X-Men: The Age of Apocalypse Volume 1 Alpha written by Scott Lobdell, Mark Waid, Jeph Loeb, Warren Ellis, and others
Charles Xavier, better known as Professor X, has a mutant son maned David Haller. Haller is better known as the villain Legion, so named because he has multiple personalities who all have different mutant powers. Legion has been in a coma for years. Unfortunately, the coma has been quite restorative, reintegrating his various personalities and powers in one semi-sane person. And he's woken up. After considering the situation, Legion decides that his father's dream (of mutants and humans living together in harmony) has been frustrated by Erik Lehnsherr, aka Magneto. To fix the situation, Legion goes back in time to when Charles and Erik first met with the intent to kill Erik. In the fight, he kills the wrong guy, thus generating a world in which Charles Xavier never had a chance to work on his dream. Erik, strangely enough, picks up his friend's idealism and leads a group of mutants in the new version of the future/present.
And the new future is pretty terrible (outside of Quantum Leap, has time travel ever fixed anything?). Apocalypse has organized his own group of mutants and taken over North America. Humans are either eliminated or sent to work camps or gathered for genetic experimentation. Mutants are either recruited or eliminated. Magneto leads the X-Men in the fight against Apocalypse. But it's an uphill battle. Apocalypse has plenty of evil henchmen, like Cyclops and Beast (who were good guys in the "normal" reality), aiding his plans to expand his empire outside North America.
The book is an interesting "what if" scenario that is played out on a grand scale. In addition to completely altering the history, the story also changes the allegiances and appearances of many characters. Jean Grey and Wolverine (who is know as Weapon X since he was never recruited away from that program) are a couple who run missions for Magneto. Rogue is Magneto's wife and they have a son, Charles, who is a toddler hidden at the ruins of Xavier's Westchester mansion. The shifts for the characters are fun but without some extensive knowledge of X-Men history it can be hard to follow. The other challenge is keeping track of the various plotlines. And the story doesn't end with this fairly thick volume. I'm interested enough to keep going.