10 Theories How Wolverine Can Fit Into X-Men: Apocalypse
6. Mystique Goes To Free Him
While the dialogue used in the trailer to introduce Wolverine suggests the team finding Logan was a bit of a surprise, it is possible that he was actually the focus of the mission.
After all, even though Jean and Storm don't know him, Mystique and Quicksilver do and, with Xavier out of the picture, they would naturally go to the other guy who actually seemed to have some semblance of control and understanding of the future. And, because she posed as Stryker, Mystique will either know explicitly or have the clues to be able to figure out where he's been held.
What part Logan can actually play in the plot is limited, of course, given that he doesn't stick around, although that may be because the skill they want him for - clairvoyance - was "lost" when the new timeline started (something that will form a separate theory in a minute).
This idea actually feels incredibly tight, instantly providing an explanation for the Mystique-Stryker at the end of Days Of Future Past and making a Hugh Jackman cameo feel purposeful, rather than just something shoehorned in out of tradition.