The setting

The end of Days of Future Past saw everything in its right place, an idyllic future in which all of the dead X-Men were alive, Professor X was still the head of the school, and Wolverine himself was a professor. Then came X-Men: Apocalypse, with the Wolverine cameo and, tied to it, the tease of Mister Sinister.
According to James Mangold, Logan will take place five or six years after the Days of Future Past ending. And that’s because he wanted to break free of everything said about the character up to that point. According to the director, this gave him enough space to make a Wolverine movie that was solely about Wolverine, a fresh movie that doesn’t rely on the previous ones (Mangold talks about elbow room). And this is great, since the X-Men timeline is not exactly understandable.
As far as Mister Sinister is concerned, the director also said that the character won’t appear in the film, for the same reason. However, he also says that Sinister is a bit too outlandish for what he has in mind for the final installment of this franchise.
