There was a series (two, actually) called "X-Men Forever" where Claremont wrote the stories he planned to write until he got shitcanned from the series after issue 3.
Tl;DR; Mutants are dying from "burnout"; the more they use their abilities, the more they shorten their life. Chucky gets imprisoned in space by the Shiar for crimes against their kingdom. Wolverine gets fried to death by Storm, who is evil now (something to do with evil clones). Sabretooth gets his eyes melted and can't grow them back due to burnout, and joins the team to avenge Wolverine, who is revealed to be his son. Due to a power fuckup caused by Fabian Cortez, Kitty ends up with some of Wolverine's healing powers and one of his claws. Nightcrawler and Rogue end up swapping powers and appearances. Mystique also joins, and her shifting powers make her immune to burnout since she "resets" her cellular structure every time she morphs. Gambit switches to a suit and tie with red shades for some reason, and now looks like Cyclops if he was starring in American Gigolo.
As for the main X-Men canon, Xavier turned Krakoa into it an independent sovereign nation. It produces drugs that extend lifespans by 5 years, cures cancer, and cures mental disabilities. Mutants that died can be resurrected by 5 particular mutants using the abilities together to clone a new body and download "backup" copies of their minds into them. Scarlet Witch faked her death as part of an elaborate ploy to redeem herself by allowing ALL mutants that died prior to their minds getting backed up by Cerebro (like Thunderbird) to now be resurrected as well. Twelve mutants run everything as the Quiet Council: Xavier, Emma Frost. Hope Summers, Destiny, Mystique, Kate Pryde, Mister Sinister, Exodus, Nightcrawler, Storm, Sebastian Shaw, and Colossus. Magneto, Apocalypse, and Jean Grey retired from seats recently.
This all stemmed from Moira revealing that she is a mutant with two powers: to be shielded from detection as a mutant (including psychics, who can only "see" her past memories if she allows it) and that every time she dies, that timeline dies with her and then she relives her life all over again while retaining all memory of her past lives. At this point, she has "lived" 10 lives, all where she failed to stop humans from extermination the mutant race, and its apparent that mankind will combine with the Phalanx to evolve into "Homo Novissima", and that no matter what she tries, humans and machines always win. Unfortunately, her plot involved faking her death, staying hidden under the island, and making herself known only to Erik and Chuck, and preventing all precogs (like Destiny) from getting resurrected. This back fired badly when Mystique tricked her way into getting Destiny brought back. Them they exposed everything that Mags and Chucky covered up, depowered Moira, and this eventually led to Moira joining forces with Nimrod and Omega Sentinel.
Oh, and it's a crime to kill humans, which results in being buried alive under the island forever, where Sabretooth is now rotting. Also, Nightcrawler declared "LET US FUCK" and make more mutant babies.