Since the release of Logan, there's been a lot of discussion about whether the movie takes place in the X-Men: Days of Future Past reality, the X-Men: The Last Stand world that The Wolverine was set in, or just somewhere free of any sort of continuity. During a recent chat with Empire Online, director James Mangold appeared to further muddy the waters when he revealed a Jean Grey deleted scene.
During Logan's dinner scene, the conversation was going to turn to Wolverine's former flame with Professor X making a startling revelation about what happened to the powerful psychic mutant.
"I sketched out different conversations for that scene and one of them went to a much darker place. Mrs. Munson asks Logan if he’s married, and Charles says he was, but he killed her. Of course, he wasn’t really married. But what that then spawns is Charles waxing poetic about Jean Grey. The problem was, it created an incredibly powerful lead brick in the middle of the only moment in the movie where there was a breather. Even I, with my taste for the dark, felt that it was one too many. I think [the deleted scene] will make it to the Blu-ray."
Wolverine obviously killed Jean at the end of X-Men: The Last Stand, but Xavier was dead at that point, so how would he know that? Well, he did wake up in that other body before finding Logan at the end of The Wolverine! Perhaps these are just the ramblings of a confused old man, though one theory is that Logan was forced to kill his fellow X-Men after Charles' meltdown led to them being left in horrible pain. Unfortunately, this movie's place in the X-Men Universe is one of many unanswered questions.