In the 21st century (the year is 2013), an adult Kate Pryde-Rasputin makes her way through the dangerous remains of a destroyed Manhattan to rendezvous with Wolverine. But it's the last place the Sentinels would be searching for the X-Men. She falls down a trap door and is being threatened by some thugs when Wolverine shows up.
Wolverine - Colonel Logan - has been in the Canadian Resistance Army. He reports that once the Sentinels move out of North America, the other great powers will launch a nuclear attach. He give her the last component of the "Jammer" for her to smuggle back into the camp. Phase two of their plan begins at midnight, when Logan busts them all out.
In this future, people are required to wear a letter that labels what they are - H for human (clean of mutant genes and allowed to breed), A for Anomalous (possess mutant genetic potential and prevented from breeding) and M for mutants (who are hunted and killed)
Kitty returns to the South Bronx Mutant Interment Center, carrying medical supplies. After being interrogated and searched by a Sentinel, she's allowed the enter and passes through a huge cemetery, with tombstones naming most of the members of the X-Men and Fantastic Four.
Only four of the X-Men remain -Wolverine (Logan), Kate, Storm (Ororo Munro), Colossus (Peter Rasputin, Kate's husband). They are joined by Franklin Richards (the last remaining member of the Fantastic Four) and his girlfriend, Rachel.
She reports back to them what happened and about the plan. They're joined by Magneto, who's in a wheelchair, who tells them they don't have any choice. If they don't do anything, the world will be at war.
Magneto tells Rachel that so much depends on her. She tells him she won't fail and they can start once the Jammer is ready.
Peter asks Kate if they should be toying with the fabric of reality like this, and if it works, what will happen to them? Kate replies that with billions of lives at stake, they have to take the risk. After everyone they've lost, if changing the past holds any chance of saving them, they have to do it.
Later, Magneto goes to check on Franklin's progress with the Jammer - which neutralizes the inhibitor collars they all wear to prevent them from using their powers. He finishes making the final adjustments and they're ready.
Kate lays down on floor and Rachel sits behind her and tells her to relax. Their minds become one and Kate's soul is sent hurling back through time.
October 31, 1980 - the Friday before the closest presidential election in recent memory. Kitty enters the Danger Room to deliver a message from Nightcrawler, but the session had already started.
Storm, Wolverine, Colossus and Angel are in the middle of fierce training session and immediately have to save Kitty. Nightcrawler teleports in in the nick of time to turn the session off before Kitty and Peter are crushed.
After being told off by Ororo, Kitty prepares for her first session in the Danger Room by herself. Kitty is able to face all of the challenges by phasing and keeps her eyes closed the whole time.
Suddenly, Kitty comes face-to-face with her future self and collapses. The X-Men rush to her, and can't figure out what happened. She's taken to the infirmary.
She wakes up, hugs Nightcrawler and overwhelmed at seeing him alive. The X-Men are surprised by this, since Kitty has always been scared of Kurt. Kurt tells her that she isn't making any sense and she needs to rest, but Kate doesn't have time. She tells them that she can't believe that Rachel actually pulled this off. Peter asks who Rachel is. Kate tries to explain to them her future self is inhabiting her body, but Ororo thinks she's just confused after having such a rough time in the Danger Room.
Kate is able to convince them she's telling the truth by recalling the events that lead to her future - the assassination of presidential candidate Senator Kelly, along with Charles Xavier and Moira McTaggert, by the Brotherhood of Evil Mutants happens that day. That event sets in motion events that culminate in nuclear war.
They take Kate to Washington DC in Warren's private jet.
During the plane ride there, Kitty further explains how Kelly's death effects events in the future. People began to fear and hate all mutants, which enabled an anti-mutant candidate was elected President who passed the first Mutant Control Act. But that was struck down by the Supreme Court as unconstitutional. As a result, the government reactivated the Sentinel program to wipe out all mutants and even all super-beings (including the Avengers and Fantastic Four).
Kate breaks down while telling them that the X-Men lost the fight and most died. Seeing them all alive is too much for her to bear.
She continues that the rest of the world became more frightened of the Sentinels than mutants. She explains that one of the surviving X-Men, a telepath (Rachel), devised a plan to psychically send one of the others back in time to exchange places with their younger self and stop the assassination. Since Kitty hadn't been fully trained to resist psychic attacks, she was the best candidate.
Kate wonders what's happening back in her future, and if Logan had freed the others from the camp.
New York, 2013 - Logan, an unconscious Kate being carried by Peter, Ororo, Rachel and Franklin make their way through an abandoned subway tunnel. Magneto stayed behind the cover their escape. Suddenly, Sentinels attack and vaporize Franklin as Rachel watches on in horror.
Two Sentinels rip the Subway tunnel open and order them to surrender.
Traumatized, Rachel tells Storm that she felt Franklin die in her mind. Ororo tries to get Rachel to pull herself together since they need her.
Ray tells Ororo she won't break, and blasts the Sentinel, wanting to destroy it to avenge Franklin.
Storm tries to hit the Sentinel with lighting bolts, but it's insulated against her powers. Colossus asks Rachel to protect Kate with her life as he armors up, then hurls Wolverine at the Sentinel with a Fastball Special. Wolverine is able to penetrate the Sentinel's armor enabling Storm's lighting bolt to fry it's computer systems. Meanwhile. Colossus and Rachel are able to take out the other Sentinel.
But as they make their way through the city streets, three more Sentinels are heading towards them. Colossus pushes down an hotel on top of the Sentinels to give them time to make it to the Baxter Building - where the central controls for the Sentinels are.
October 31, 1980 - Washington DC -A woman named Raven Darkholme, who works in research and development for the secretary of defense, makes her way to a secret area of the Pentagon - where the new Brotherhood of Evil Mutants is gathered. Raven is really Mystique, the Brotherhood's new shapeshifting leader. The other members are: Destiny (a precog who can see the future), Avalanche (who can crumble any solid object), Pyro (who controls fire), and Blob, who they have just helped escape from prison.
Destiny had foreseen a new element that might cause problems for them, and Blob has issues with taking orders from a woman. They all bicker but Mystique ends it, telling them that it's time for them to strike.
Across town, Charles and Moira are at a Senate hearing on mutants. They notice Ororo, Kitty and Peter standing in the back of the room. Charles first mindscans Ororo, then Kitty.
Senator Kelly continues to question Moira about mutants, and the place for ordinary humans in a world of super-beings.
Suddenly, a hole is blasted into the wall behind them by Avalanche, and there stands the new Brotherhood of Evil Mutants. The X-Men (Colossus, Wolverine, Storm, Kitty, Angel and Nightcrawler) appear in uniform. If the Brotherhood wants to harm the Senator, they're going to have to go through them.