Getting back on topic...I'd posted my speculations (read: advance fanfiction ) on how I'd like the MCU X-men reboot to pan out. I've changed my mind about a few things since then, and the more recent rumors (and subsequent discussions we've had here) have also inspired me. So...here's my new take on the reboot film. This time I've not tried to do a full plot breakdown (I'm not a professional screenwriter after all!) but just strung together some of the broad ideas I have.
UNCANNY X-MEN
The film begins with a quick prologue in NYC, amidst news reports about a string of mysterious robberies by superhuman beings, as well as speculations about the existence of 'mutants' as the next stage in human evolution, which government sources deny. We have a warehouse where a gang of mutants - Toad, Blob, Avalanche, Vanisher and Unus - who're behind the robberies, before they're confronted by the X-men - Cyclops, Storm, Marvel Girl and Beast (the latter in his pre-furry form). The X-men manage to take out most of the Brotherhood members, which the final blow being struck by Morph, who was disgused as one of the gang midway through the fight. Professor Xavier's telepathic voice then orders them aboard the Blackbird, telling them that the 'propert authorities' will deal with these criminals.
Flashforward five years later. The existence of mutants is becoming more widely known and we see the early stages of anti-mutant hysteria beginning to form, with newly-elected Senator, Robert Kelly, starting to propose a Mutant Registration Act. Professor Xavier, as a renowned geneticist and mutant rights campaigner, has been trying to steer the conversation in the right direction among government and media circles, but seems to be fighting an uphill battle. The X-men have long been disbanded (under circumstances that will later be revealed), and Scott is the only one left at the Mansion. While he's loyal to Charles even he's starting to chaf a little with Xavier's current more diplomatic and less 'active' approach.
Scott goes out on a date with Jean, who's now a college student, and we get some hints from their conversations about Scott's frustrations, their mixed feelings about Xavier, and the reasons why the X-men disbanded. However, they're suddenly attacked by what looks like a black ops unit from a PMC. Jean ends up getting captured but Scott gets away. He gets back to the Mansion to discover that a band of mutates - the Nasty Boys - have successfully taken the Professor in his absence.
In a bid to find out what's going on, Scott tries reaching out to other former members, to discover that Hank's already been taken and he can't find Kevin anyway. He does track Ororo, who's back with her tribe in Kenya, and convinces her to help him find the Professor and the others. Though Ororo has some misgivings about the X-men, she agrees to return with Scott to the States to help her friends and former mentor. They learn that a lot of other mutants have gone missing as well across the country, and beyond. Realizing that they'll need help, Scott opens up some Cerebro files Xavier was maintaining of potential recruits, and he and Ororo reach out to them. In the Canadian Rockies, they meet Laura Kinney (played by Dafne Keen of course!) In NYC, they rescue Piotr Rasputin, a mutant coerced into working for the Russian Mafia. Outside a monastery in Germany, they rescue Kurt Wagner from a mob.
The next act is the newly formed X-men - Cyclops, Storm, Wolverine, Colossus and Nightcrawler - traveling the globe investigating the mutant disappearances. Along the way, there is a sequence where they encounter the Morlocks (and maybe we get a version of the Storm-Callisto duel) and learn how some of the Morlocks were killed while others were abducted. We also get a scene with Scott meeting a certain FBI agent, Fred Duncan, who had links to Xavier, and who reveals that some of the data he had on the X-men, and other mutants, may have found its way to the Essex Corporation, which is the key to what's happening.
We also slowly learn about the reason why the original X-men disbanded - Morph discovered Xavier's tie to Fred Duncan and the FBI, and how the mutant criminals the team was capturing were being imprisoned in black-sites and studied. The X-men are furious to learn about how Xavier didn't tell them about this aspect of their missions, and the fact that they were essentially capturing fellow mutant for the government. Xavier contends that this collaboration with the system was the only way he'd be able to maintain the Institute without the government's interference and help mutants. Scott, while feeling betrayed by the Professor, still sides with him and admits that he did what was necessary, while Jean, Ororo, Kevin and Hank walk away. Now, they discover that all along, Xavier and Fred Duncan (along with Robert Kelly) were pawns of larger forces, led by the mysterious Nathaniel Essex AKA Mr. Sinister, and his eugenicist experiments with mutant DNA to create the 'perfect beings'.
The X-men manage to track Essex's hidden lab to the island of Krakoa, where they have a showdown with the Nasty Boys and also free many of the captured mutants (with Hank having mutated into his blue furry form due to Essex's experiments). Jean, Xavier and Beast join the new X-men in the final battle against Sinister, and discover that their ex-teammate Morph was years ago corrupted and brainwashed completely by Sinister. We also learn that Krakoa itself is a 'mutant', a living island kept under Sinister's control, which is now broken. Krakoa consumes Sinister and his facilities, with Morph also seemingly dying in the process.
In the aftertmath, the activities of the Essex Corporation have been publicaly exposed, but all the events throughout the film have only fuelled anti-mutant hysteria further. The X-men are needed now more than ever, even as Xavier re-opens the school fully, with many of his new recruits being some of the young mutants rescued from Krakoa. Beast leaves the team (and may end up joining the Avengers...who knows?) while Jean stays.
There are two post-credit scenes. One in which a mysterious figure is seen watching a news-report about the Essex Corporation and the government's complicity. He raises his hand and a very familiar helmet levitates into it. The second sees Laura travel to Madripoor where she talks to a hidden figure in the shadows, telling them how she's found a family with the X-men, just like the other person did. The other person reveals themselves to be none other than Logan (played by the one and only Hugh Jackman) who tells Laura that he won't be joining her for now, and that its her turn to be an X-man. He's got other things to do in the meantime...
Okay, that ended up being virtually a full plot breakdown...