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Second. DOFP was the first

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We don't know that the X-Men are dead.
They could be in hiding, they could be off world or in another dimension, they could have travelled through time, they could have retired and quit the superhero business, they could have joined other teams, or they might be busy with another threat. All we know is that Wolverine and Professor X aren't with them, wherever they are.
I think they've had their memories erased by Professor X. Mister Sinister is a telepath who can read minds, and with Donald Pierce and his Reavers hunting the X-Men, along with Mister Sinister telepathically scanning for them and guiding the Reavers, Professor X probably thought the only way he could save his X-Men was to erase their memories, implant new ones and scatter them across the globe. It just didn't take on Wolverine because of his regenerative abilities, and it only partially worked on himself because in the back of Charles' mind he knows what he did. This is similar to what happens in the comics when the Reavers come for the X-Men, with Wolverine being the last known member of the X-Men alive (around Uncanny X-Men #251).

my guess is since in this timeline there were no sentinels capable of eliminating mutants, humanity instead created a virus which targets mutants directly.
it also what causes wolvie to lose most of his healing factor which is why he aged rapidly.
Xavier is immune to the virus because he's not in his original body anymore but instead transferred his mind to the body of a brain dead guy who also happens to look exactly like him and also paraplegic

I don't think they are all dead, there just seem to be alot less of them now for some unknown reason.
Mutant births are much lesser now according to TheWrap article.

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