X-Men Apocalypse: 11 Biggest Questions Answered
9. How Did Wolverine End Up In The Weapon X Program?
The Question: Considering that Days of Future Past ended with Mystique rescuing Wolverine while disguised as William Stryker, how the hell did he still end up legitimately imprisoned in the real Stryker's Weapon X program?
The Likely Answer: This is a tough one considering it really doesn't seem to make much sense at all, but perhaps Mystique initially placed Logan in Alkali Lake as a sleeper agent of some sort, to gain intel, but for reasons unknown, didn't bail him out.
Yeah, it's a hokey explanation, but then this is one of those truly baffling issues that will probably never be satisfyingly explained because it just doesn't seem to cohere. We'll go with the simplest solution: Mystique did set Logan free at the end of Days of Future Past, but he ended up captured by Stryker sometime down the line anyway.