The crux of the plot involves Wolverine travelling in time to thwart an assassination committed by Mystique. It is noteworthy that even though these two main characters had a big fight scene in X-Men (2000), they never interact with each other in this film, either in the Theatrical nor Extended Cut. The closest they get to a meeting is during the Paris conference where Raven is electrocuted and Logan has a mental breakdown, and in the final scene where Logan is unconscious with Mystique supervising his rescue. However, the two of them do not exchange a single line of dialogue, which raises the question of why Mystique would save Wolverine from the bottom of the river in the final scene. There is, however, a non canonical answer to that. In a deleted scene, Raven returns willingly home and she has a frank discussion with Hank, Charles and Logan about the future repercussions of her actions. This meeting between Raven and Logan takes place in the kitchen of the Xavier mansion. Although it was deleted from both prints of the film, it serves as the only reason for Mystique to go to all that trouble to save Logan, a mutant otherwise unknown to her.

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