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Mister Sinister is one of the few major X-Men villains that hasn't appeared in a theatrical movie yet, but the X-Men series is taking steps towards introducing him. He was referred to earlier this year in the X-Men: Apocalypse post-credits scene through a briefcase labeled "Essex Corp," referring to his birth name, Nathaniel Essex. Then Bryan Singer suggested in the X-Men: Apocalypse audio commentary that Mister Sinister will appear in Logan, leading some to think that he might be that movie's main antagonist. However, it appears that won't be the case, though that doesn't necessarily mean he won't have any kind of presence in the third
According to The Wrap, Mister Sinister will not appear in Logan. However, there's still a chance he could appear in the movie's post-credits scene, thus setting him up for a full appearance later down the line. As for the folks who speculated that Richard E. Grant's "villainous mad scientist" character was Mister Sinister, the report instead identifies this person as Dr. Zander Rice, the man behind Transigen and, if he's like his comic book counterpart, X-23's creator.
If this information is correct, the X-Men franchise is obviously taking a slow burn approach with Mister Sinister. First there was the briefcase in X-Men: Apocalypse, now there's the chance that we could see him in Logan's post-credits scene, although there's no guarantee that he would be fully seen. They could just shroud him in shadows, extending the tease towards his eventual debut. At this point, it almost sounds like Mister Sinister is intended to function as the X-Men cinematic universe's Thanos, i.e. an overarching villain who poses a threat to all corners of this fictional world, but has to be set up in small doses before getting a chance to shine.
As it stands now, the only thing we know about Mister Sinister in this universe is that his corporation secured a vial of Wolverine's blood from Weapon X in the early 1980s, but considering the experiments that Transigen is running on young mutants in Logan, it wouldn't be surprising if Nathaniel Essex was somehow connected to the organization. Regardless, whether or not Sinister appears in the Logan post-credits scene, that still begs the question of which movie he'll get to be the main antagonist. New Mutants seems like the best bet since it's the next X-Men team superhero movie that's coming down the pipeline, but other options could include another main X-Men movie or the long-struggling Gambit (Deadpool 2 seems unlikely).
Then there's the question of how Mister Sinister's slowed aging will play into these movies. After all, Logan takes place in the future, while it sounds like New Mutants and the next X-Men movie will take place in the past. That means even if these heroes defeat him in the 1990s (as an example), he'll still be around decades later to cause trouble. The sooner we can get some answers regarding this pale-faced evildoer, the better.
We'll find out what role, if any, Mister Sinister will play in Logan when the movie is released on March 3, 2017.