In a sequence that appears to be as much a setup for the upcoming Wolverine 3 as anything else, X-Men: Apocalypse finds Wolverine in the hands of William Stryker and the Weapon X program, as has been told previously in the X-Men films.
Secondly, the word is that Weapon X will actually be the title of the third Wolverine movie, meaning the Wolverine-related parts of X-Men: Apocalypse, including the film’s post-credits sequence, will likely play directly into that plot.
Upon his release, Weapon X reacts as you’d likely expect, brutally murdering through those that kept him prisoner.
While we’ve seen Wolverine go through the entire Weapon X procedure, both in flashback’s from X2 and the opening of X-Men Origins: Wolverine, it appears that seeing it again here may be important.