The continuity of the X-Men film franchise has had its share of inconsistencies and puzzling moments for years now (even more so now that Deadpool's out there roaming free in the timeline), but perhaps no other film has introduced as many new wrinkles as Days of Future Past. The 2014 film -- which saw the X-Men battling sentinels in an apocalyptic far future and attempting to stop their proliferation in the 1970s, with Wolverine as the time-traveling bridge between both -- set out to fill in a few things about the series' timeline and make a few things right for fans after X-Men: The Last Stand, but in the process it might have raised even more questions than it attempted to answer. Now, director Bryan Singer is trying to clear up at least one.
Specifically, a moment at the end of the film when Wolverine is fished out of the Potomac River after being bound up in metal by Magneto. After he's rescued, Wolverine is brought before William Stryker, who takes him into custody, but not before his eyes flash yellow to indicate that Stryker in this case is really Mystique in disguise. The real Stryker, of course, runs the Weapon X program that ends up giving Wolverine his adamantium skeleton and adding a huge amount of trauma to his life. Stryker also appears again (chronologically) as the main villain of X2: X-Men United.
So how does Mystique figure into that? If you watched Days of Future Past in 2014, the implication was that she would either save Wolverine from his Weapon X destiny, alter it, or both, but none of that happens. By the time X-Men: Apocalypse rolled around Mystique (now back to calling herself Raven) was traveling the world and saving mutants to recruit them for the Xavier Institute. Wolverine does appear in the film, but only as a cameo, and very clearly in his aggressive Weapon X form. So either Mystique didn't help him at all, we never saw the full extent of her plan, or the thread was just never picked up on. After seeing questions about the Days of Future Past moment pop up on Reddit, Singer responded to the question on his Instagram page.
Yes, after her redemption at the end of of Days of Future Past, Mystique does take up a new path of covertly aiding mutants around the world, but it's not really clear exactly how she helped Wolverine here. Unless there are pieces in the timeline that we never got to see, Wolverine ended up exactly where he would have been anyway. Perhaps Mystique tried to help him and failed, only adding to her need to keep trying, or perhaps Wolverine pushed her away. In any case, Mystique carried on her mission even if it didn't work out with Wolverine and Stryker. Fill in those gaps in the timeline however you like, because with Jackman retired as Wolverine and the X-Men timeline moving on to the next film, we'll likely never revisit that territory.
The X-Men will next appear onscreen in Dark Phoenix, set to arrive February 14, 2019.