10 Theories How Wolverine Can Fit Into X-Men: Apocalypse

5. Alakali Lake Is Important To Apocalypse

It's important to remember that this is all happening in a movie called Apocalypse, so while it's easy to speculate about Wolverine and the surrounding sequence in isolation, it does need to fit into the wider scope of the film. With the Stryker angle you're bringing in a supporting villain, but there's nothing to suggest it won't be more linked into Apocalypse's big scheme.

This sequence appears to be after Charles has been taken by En Sabah Nur, but before the first mutant has enacted his doomsday plot, so what if in between he needed to visit Alkali Lake, either to find some MacGuffin or free allied mutants. You could then have the X-Men exploring the base in an attempt to figure out what he's up to, chasing him from a few steps behind, discovering the extent of Stryker's scheming almost by accident.

I am more inclined for the Wolverine scenes to be a tangent subploy, with the middle part of the film concerned with Mystique assembling the X-Men while Apocalypse operates unencumbered, but it'd still hardly be a shock if we see Logan as a by-product of the big bad's scheme.