Where have all the Mutants gone?

[Captain Picard's Hair]

There are a number of possibilities as to what happened to the mutants in the future of the X-Men universe as depicted in Logan. But that's nothing next to their disappearance for thousands of years and subsequent re-appearance. In Apocalypse, it turns out there were mutants (plural) in the ancient past. Apocalypse himself couldn't have been the only one, as the opening scene depicts at least five others (his 'horsemen' and a fifth, the one with healing powers who became the new host for his consciousness) and he seems to carry the accumulated powers of several other mutants already by then. Then there's no sign of them until the fairly recent past (at least whenever Wolverine and brother Sabertooth were born or earlier). The four horsemen were killed in the opening scene when (new) Apocalypse himself was buried (and old one died) but even if they were the only six around at the time, this mutant phenomenon is obviously a recurring thing (since, well... it recurred). When they came back they came in large numbers too.

Apart from it's merits as a story (and eventually a film) this whole affair just makes the X-Men universe (whether comics or film adaptations) more confusing than it already was.

[Graham Kennedy]

At this point I pretty much just take every X Man movie as a complete reboot of the franchise. Any givne film might have some elements in common with previous ones, but I don't regard any of them to be sequels as such.

[Mikey]

Is Logan the first released as a Marvel Studios production, rather than just "in association with?" If so, that would explain some differences as well supposedly planting a franchise anchor in the MCU. In general though, having seen neither this new one nor the Apocalypse one, I can say that in the comics universe Apocalypse - while generally starting with mutant stock - used various artificial methods to transform people into more stabby, kill versions for their role as a Horseman.

Also, recall that in Origins, at a point roughly 45 years before now, there were enough mutants around from which to hand-pick a spec-ops team as well as a personal staff... and a decade or two later, what seemed to be hundreds to imprison and use for the Deadpool project.

[McAvoy]

I suspect that smaller population means less mutants. Infant mortality might play a factor. Those with powers might have played a part in the mythology we have. Werewolves might have been a Beast-like mutant, Dragons, gods and so forth.

[Captain Picard's Hair]

Is Logan the first released as a Marvel Studios production, rather than just "in association with?" If so, that would explain some differences as well supposedly planting a franchise anchor in the MCU. In general though, having seen neither this new one nor the Apocalypse one, I can say that in the comics universe Apocalypse - while generally starting with mutant stock - used various artificial methods to transform people into more stabby, kill versions for their role as a Horseman.

Also, recall that in Origins, at a point roughly 45 years before now, there were enough mutants around from which to hand-pick a spec-ops team as well as a personal staff... and a decade or two later, what seemed to be hundreds to imprison and use for the Deadpool project.

Yep, they rapidly became plentiful, just adding to the conundrum. Even taking Apocalypse on it's own isn't too helpful since it has ancient mutants, (plentiful) modern mutants, but still implies there were no known mutants in the many years between.

McAvoy has a good suggestion though. That might be something a clever writer could tackle.