The end of DoFP is sinister!!!
We see Wolverine being fished by Mystique in the Potomac River, in 1973, during the events of DoFP. Ten years later, Wolverine is part of the Weapon X project, who is run by Stryker. Mystique, in the other hand, is travelling the world to save mutants and, sometimes, deliver them to the Xavier's school. From DoFP to Apocalypse, the history of Wolverine seems pretty obvious and predictable, but Mystique's seems mysterious. She was a mutant savior... a HERO! So, what did she did with Wolverine and how did he get in the Weapon X?
Some theories suggest that Mystique saved Wolverine from the Potomac River, freed him, and, after that, Stryker captured him, and did whatever he wanted. This seems plausible... but I don't like it.
Another (better) theory says that Mystique captured Wolverine and delivered him for Stryker, in order for Stryker to never capture more of his fellow mutants. A promess that Stryker kept (at least until 1983). But why, Wolverine? What's the relationship between Wolverine and Mystique? Did Mystique and Wolverine had a relationship before 1973, that led to the behaviour of Mystique that we see at the end of DoFP?
It really seems one of the darkest mysteries of the X-Men movie franchise! I would like to see other theories and thoughts...