WARNING: Major spoilers for Dark Phoenix ahead.
X-Men: Dark Phoenix doesn't actually contradict the glimpse of the future shown in X-Men: Days of Future Past. There's a sense in which X-Men: Days of Future Past was the biggest X-men movie of the entire franchise. It ended with an optimistic glimpse of the future, with Wolverine learning that he'd created a new X-Men movie timeline in which the world was at peace. Charles Xavier was still headmaster of Xavier's School for Gifted Youngsters, and to Logan's delight, old friends like Storm, Beast, Cyclops, and even Jean Grey were still alive.
And yet, although X-Men: Dark Phoenix is part of this timeline, many viewers are complaining that its ending contradicts it. X-Men: Dark Phoenix ends with Jean Grey leaving the Earth, apparently committing suicide in a phenomenal burst of Phoenix fire that kills Vuk, leader of the D'Bari. In the aftermath of Jean's sacrificial victory, Charles Xavier retires, with Beast taking over the school and renaming it in honor of Jean Grey. A final scene sets up the possibility that a regretful Xavier will settle down on Magneto's island nation of Genosha. At first glance, all this doesn't really seem to connect all that well to X-Men: Days of Future Past.
The key, however, is to remember that there's still a 30-year time jump between X-Men: Dark Phoenix and the future Wolverine returned to in X-Men: Days of Future Past. A lot can happen in the space of 30 years, especially in a world of cosmic forces and immortal mutants. Take, for example, the most obvious issue; Jean Grey's apparent death. The reality is, though, that the end of the film deliberately suggests she isn't dead at all; rather, she has evolved, bonding with the Phoenix Force but retaining her consciousness. A flare of Phoenix energy in the skies over Xavier and Magneto suggests she's still watching over her family. That means she could easily return, whether to help the X-Men with the next crisis or simply to be with her beloved Cyclops. Indeed, that may even explain why the Jean Grey School is renamed again; no doubt Jean herself would be quite weirded out by it.
Likewise, just because Charles Xavier has retired, it doesn't mean he's gone for good. In fact, the very idea of Xavier retiring to Genosha is lifted straight from the comics, and it didn't take Charles long to return to the X-Mansion. In the comics, Magneto's nation proved somewhat ill-fated, with rogue Sentinels wiping out its mutant population; it's entirely possible something similar will happen in the cinematic timeline as well.
Only one other thing really needs to happen in order to perfectly link X-Men: Dark Phoenix's end to the future timeline seen in X-Men: Days of Future Past. Sometime in this 30-year period, the X-Men have to cross paths once again with Wolverine, who they freed from the Weapon X Project in X-Men: Apocalypse. It's impossible to say whether or not this timeline's encounter with Wolverine follows the same pattern as the one shown in the original timeline ofin 2000's X-Men. The reality is that Magneto, at least, seems to be committed to a very different path. However things are destined to play out, though, it's safe to say Logan joins the X-Men.
X-Men: Dark Phoenix writer-director Simon Kinberg has assured viewers that the two X-Men films tie together without breaking the timeline, but said it was ultimately more important to provide a culmination to the series of films than it was to connect every little dot. While it's clear there's a few gaps for the viewer to fill in for themselves, Dark Phoenix does provide a clear endpoint to the X-Men movie franchise, without outright contradicting X-Men: Days of Future Past.
More: Dark Phoenix Has A Plot Hole So Big It Breaks X-Men: Apocalypse
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