Warning: SPOILERS ahead for Logan
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Comic book-style continuity can be a bizarre thing, which is why very few movie franchises (even those adapted from comics in the first place) bothered to attempt it prior to the establishment of the Marvel Cinematic Universe. In fact, some of the most bizarre continuity experiments have taken place in franchises belonging to other genres entirely: The Highlander series had to retcon away a new backstory conceived for its poorly-received second installment, Terminator Genisys rebooted and remixed its own timeline, and even the Child's Play franchise set its third episode in the then-future (which then became the "real" present when Part 4 took almost a decade to arrive).
But the superhero genre has been reclaiming its territory in this regard over recent years, spearheaded by Marvel but now followed by the emerging DC Extended Universe and others. However, when it comes to replicating (for better or worse) the often maddening temporal contradictions of the original comics, Fox's X-Men series towers above the rest. Over the course of ten (or so, depending how you count it) films, the X-Men movies have featured time-travel, alternate futures, retconned backstories, and a litany of inconsistencies that have yet to be addressed at all. Now, Logan - the presumed final outing for Hugh Jackman's Wolverine - arrives, taking place in a dystopian future so different-feeling from anything else in the franchise that when Jackman described it as taking place in an "alternate universe," some didn't even bat an eye.
But with the director later walking back that statement, the X-Men franchise now sporting at least one confirmed alternate-universe project on TV with Legion and veritable mountain of continuity questions already lingering in the background; what really is going on here?
A DYSTOPIAN FUTURE
That Logan looks and feels different from the other X-Men movies isn't in itself some kind of "evidence" that it's not actually part of the same continuity. Plenty of franchises feature installments that take a tonal or aesthetic shift to keep things fresh, and the X-Men series has already done so with the comedy-centric Deadpool and the retro-styled First Class and Days of Future Past installments. However, it is worth noting that Logan's future is not simply visually distinct from the rest of the series - it seems to have deliberately stripped out any sense that the other films even happened.
Some of that is explained as the film goes on: For separate reasons, the Mutant species has effectively died off and the X-Men are all gone save for Wolverine and Professor X. What we hear about Mutants from the incidental/ambient dialogue that carries much of our early exposition (before anyone starts openly discussing the plot) heavily suggests that the world has largely "moved on" from the issue, and the presence of "old" X-Men comic books detailing what Logan describes as embellished and/or outright fictional adventures of the team further implies that the whole prior era has slipped into the realm of legend.
All well and good (especially since the fruitlessness of looking back in regret is a key theme of the film) but it still doesn't explain why certain things haven't managed to hang around - or why they aren't referenced to begin with.
MISSING PIECES
In the film-proper, Logan and Xavier are attempting to help Laura (Dafne Keen), a laboratory-engineered preteen female "daughter" cloned from Logan's own DNA, escape a bionically-enhanced militia called The Reavers hunting her down at the behest of the sinister Transigen Corporation that created her as part of a super-soldier "mutant-engineering" program referred to as X-23. Eventually, it's revealed that Transigen's founder Zander Rice is the son of one of the technicians who transformed Logan into the Wolverine (and was killed during his escape), and that he also engineered the extinction of "natural" Mutants by disseminating gene-altering additives into the world's food supply. While not mentioned in the film proper, it's been suggested (in official contexts) that Transigen got its supply of Mutant genetic samples from The Essex Corporation (read: Nathaniel Essex, aka "Mr. Sinister"), who were shown collecting Wolverine's blood samples from the Weapon X Program in a bonus scene from X-Men: Apocalypse.
But wait - why did Transigen need to go through all that trouble? They'd be the third corporation to try and eradicate Mutants, after all. Bolivar Trask tried to do it in the 1960s (X-Men: Days of Future Past) and had developed both mutant-tracking technology and a fleet of giant robots who could use it to act as enforcers, and Worthington Labs developed a Mutant-gene "cure" by replicating the mutation-neutralizing powers of Leech. Why is Transigen remaking technology from scratch that prominent predecessors already laid a ton of groundwork for? Heck, according to the events of Deadpool you don't even need to muck around with DNA samples - Ajax's rebooted Weapon X initiative had figured out how to induce "latent" mutations by subjecting volunteers to extreme physical stress.
The short answer, obviously, is that these are fictional films and can't be expected to keep track of every random thread (example: have The Avengers weighed in at all on the once-again very public S.H.I.E.L.D. agency being briefly co-led by Phil Coulson - a man they saw die?), but more practically they remind us that the X-Men series was already juggling alternate timelines.
PARALLEL TRACKS
The first three X-Men movies take plus in succession one after the other with the fourth (in release-chronology) film, X-Men Origins: Wolverine taking place from the 1880s up through the 1970s. In that film, Wolverine gets his adamantium skeleton from Colonel Stryker, escapes under his own power, rescues a collection of Mutant abductees including a teenage Scott Summers and meets a "younger" Professor Xavier as played by Patrick Stewart. But X-Men: First Class, released two years later, is set in the mid-1960s and seems to "overwrite" both Origins in its entirety and certain key aspects of X-Men: The Last Stand.
In First Class, it's established that Professor X still looked more like James McAvoy (and had all his hair) only a few years prior to Origins' setting, and furthermore that details about when the Professor lost the use of his legs, the status of his friendship with Magneto and the tenure of Hank "Beast" McCoy with the team as revealed in The Last Stand were no longer considered correct. There was no "official" explanation for any of this: The film simply presented a past that differed from what we'd been previously told the past was. The next installment, The Wolverine, ended with a shocker that left things even more up in the air: Professor X was alive again after having died on camera in The Last Stand, and he'd reunited with Magneto (who'd lost his powers in the same film but appeared to have them back here).
X-Men: Days of Future Past opted to clear the board of these inconsistencies (both planned and unplanned) with a time-travel storyline: Wolverine quantum-leaps back to the 60s to stop a series of events that will unleash a post-apocalyptic future and, as a result, wakes up in an altered version of the present where (among other things) the deaths of Jean Grey and Cyclops have been undone - presumably along with all of the events of The Last Stand.
WHICH FUTURE IS IT... AND DOES IT MATTER?
Time travel being theoretical, most science fiction stories default to one of two scenarios: Either a change in the past creates a ripple-effect that changes everything else adjacent to it (i.e. the Back to The Future movies), or it creates branching separate timelines across an infinite number of alternate realities comprising all possible interlocking outcomes. If it's the second one, that could be a plausible explanation for how Logan could incorporate some but not all of the continuity of the previous installments. It's taking place in one of many potential futures, possibly created by the reality-rewiring antics of Days of Future Past.
Is that plausible? Sure - stranger things have happened (the next installment may end up sending the X-Men to outer space, for example) but the truth is more likely that Logan's unusual nature and winking/non-committal relation to the rest of the franchise is more about hedging bets than setting up anything definitive. The X-Men franchise is in an unsure place despite the strong reviews for Logan and massive box office haul for Deadpool. Jackman (and now Patrick Stewart) are done, Apocalypse was a widely-panned dud, and the 3 to 4 "pending" projects all seem to be charting different visions of the future: A "Dark Phoenix" do-over for X-Men: Supernova (a direct sequel to Apocalypse), a younger-skewing "soft reboot" for The New Mutants, an R-rated spin-off for X-Force, and whatever Deadpool 2 decides to be about.
If Logan is already so radically different as to be a stand-alone item - mainly in order to let Jackman exit on his own terms unencumbered by franchise housekeeping - why rush to canonize it (especially on the off chance that audiences don't reward it the same way they did Deadpool) as "the" future when they haven't really figured out what the present is?
When (now confirmed) rumors leaked of Logan's plot eventually involving more child Mutants than just Laura/X-23, some speculated that they would end up being younger versions of the teenaged New Mutants characters and that the New Mutants movie itself would end up being set in the future-timeline established by Logan. That's not the case (at least, it doesn't seem to be, as none of the Mutant kids introduced appear to be known New Mutants members) but it suggests other possibilities all the same.
For one thing, even reviews that are mixed on the film tend to praise the conception of Laura/X-23, who in the comics grows up to be one of the X-Men herself and eventually inherits the Wolverine mantle. That could be an entire series in itself (with its own "possible future" continuity). It's also not outside the realm of possibility that she could run into time-traveling future Deadpool 2 co-star Cable (and maybe Deadpool himself?) and become part of a future-set X-Force - that would certainly be one way of setting that property (reportedly eyed to become an R-rated version of the X-Men hero-team concept) apart from the main series.
Ultimately, the speculation is amusing - but until the dust settles it's likely best to take Logan at face-value as a possible-future story - and, most importantly, as a movie in its own right.
