In the year 2023, the world is a dark and desolate place. Mutants have been hunted to near extinction by machines called Sentinels - robots designed with the ability to adapt to various mutant powers, and counter them in confrontations with mutants, making them virtually indestructible. The machines targetted not only mutants, but also humans that possessed mutant gene potential, as well as mutant sympathizers. Those that survive are rounded up and imprisoned in internment camps, where they will meet their eventual end. The world is left in ruins, and the X-Men are left scattered an unorganized. One group of X-Men - Kitty Pryde, Iceman, Bishop, Colossus, Blink, Warpath, and Sunspot - fight for survival by sending Bishop back in time a matter of days to warn the group of impending Sentinel attacks. This gives the group enough time to flee the scene, never being there when the Sentinels arrive. This manages to "change the future", as the others fight the Sentinels to their very deaths, buying enough time for Kitty and Bishop to complete their task. However, once done, those that laid their lives down are found alive and well when Bishop awakens in the new time.

 

A 2nd group of X-Men, consisting of Professor X, Magneto, Wolverine, and Storm, become aware of Kitty & Bishop's time traveling feats, and are able to track the group down and meet them in China. It is here that Xavier explains that the Sentinel program was created in 1973 by Dr. Bolivar Trask. Trask was assassinated at the Paris Peace Accords by Mystique. His assassination convinced the government of the need for Trask's Sentinels as a means to counter the mutant menace, and given full government support, Trask Industries was able to spend the next few decades researching and designing what would become the Sentinels that would eventually hunt mutants to near extinction. They are able to do this after capturing Mystique immediately following the assassination. After capturing her, they tortured her and experimented on her, finding use of her DNA to manipulate to create Sentinels that can adapt.

 

Kitty is hesitant, as her powers aren't strong enough to send someone back that far in time - no human mind could physically take being sent back that far. However, Wolverine volunteers for the time travel, noting his healing factor and the ability for his mind to "snap back" and heal just as fast as it is destroyed. Kitty, Xavier, and Magneto agree, and Wolverine is sent back to 1973.

 

1973 is witnessing the end of the United States' involvement in the Vietnam War. Dr. Trask is using the fact that the U.S. lost the war as part of his agenda to press his Sentinel project through Congress. It is, however, rejected on the basis that the government will not support a weapon that targets its own citizens. 

 

Out in Vietnam, Mystique seeks out and rescues a troop of mutant soldiers being prepped to be shipped to Trask Industries under the watch of Major William Stryker. This group of mutants includes Havok, who was drafted into the war. She is able to free the troop of mutants and board them on and airplane to ship them home. Upon learning where they were originally set to be headed, she seeks out Trask Industries, where she discovers that Trask is responsible for the deaths of numerous mutants - including Angel Salvadore, Azazel, Banshee, and Emma Frost - for the sake of experimentation for his Sentinel program. The motivation to assassinate Trask has been born.

 

Meanwhile, Logan wakes up in 1973 and seeks out Xavier. He arrives at the mansion, and is resisted by Beast. Here, Logan learns that Xavier can walk again, thanks to the help of a serum Beast made to treat his spine. The serum allows Xavier to walk, but it makes him loose his mutant powers of telepathy. Beast also uses the serum to keep himself human in appearance, although he can still utilize his mutation when he deems it necessary. Xavier has closed the school, a broken man, distraught after losing Raven, Erik, the use of his legs, as well as watching many of his students and teachers (including Havok) drafted to Vietnam. After initial resistance, Logan finally convinces Xavier that they need to stop Raven, and that Erik is needed to do it.

 

To find Erik, they need to break him free from a maxium security prison floors beneath the Pentagon. He is imprisoned here for his alleged role in the assassination of JFK (though it would turn out that he tried to actually save the President, as the President was a fellow mutant). They find and recruit a young Quicksilver, aka Pietro "Peter" Maximoff, and possible son of Magneto, for his super speed would prove useful in breaking Erik out of prison. After Magneto is broken out of prison, Xavier, Magneto, Logan, and Beast all head to Paris to prevent the assassination of Trask.

 

Mystique gets into a secret meeting held by Trask by impersonating a Vietnamese officer, and it is here that she makes her attempt on Trask. However, the new group of X-Men arrive just in time to stop her, distracting her long enough for Trask to get away. Things take a turn for the unknown when Erik decides to eliminate Mystique himself, and attempts to shoot her. She flees through a window, and Erik is attacked by Beast, but Magneto is still able to use his powers to fire the gun and direct the bullet after Raven, hitting her in the leg. A struggle would ensue between Beast and Magneto, allowing Mystique to get away. Logan, seeing a younger William Stryker, develops a bit of a rocky mind as all the flashbacks of Weapon X come flooding back to him. In the future, his body flails recklessly, and his unleashed claws strike Kitty, wounding her. Magneto uses his powers to restrain Logan, and Kitty is able to fight through the pain and hold Logan's mind in the past.

 

Mystique now gone, and Erik on the loose, Xavier, Logan, and Beast head back to the mansion, the future now uncertain. Raven is still seeking Trask, attempting to finish the job she started, and Erik has now determined to bring the war to humanity, believing mutants need to strike now while they still can, before the humans can unleash their weapons. Mutants now exposed publicly, President Nixon approves Trask's Sentinel project, wanting to send a message to the world that America can protect the world from the mutant threat. For a moment, Xavier's powers come back, and Logan is determined to use this opportunity to his advantage. They need to find Raven, and the only way to do that is for Xavier to stop taking the serum and use his powers.

 

Xavier attempts to use Cerebro, but his mutation, long unused, is out of control, and using Cerebro only brings harm to those he is connected to via the machine. There is an overload, and Cerebro shuts down. Xavier is convinced that everything was a mistake, but Logan gets Xavier to look into his mind. Here, Xavier sees Logan's lifetime of painful memories, his love for Jean Grey, the Weapon X procedure, and eventually having to take Jean's life. Logan insists that Xavier look deeper, beyond Logan. Xavier does, and through Logan's mind, he is able to communicate with his older self.

 

The older Xavier gives younger Xavier a glimpse of hope - showing a mansion full of students, showing the X-Men, and insisting that there is still hope in the world. This convinces Xavier that there is something still left to fight for, and he uses Cerebro again to locate Raven. He finds her at an airport, on her way to Washington, D.C. where the President, along with Trask, are to publicly reveal the Sentinels to the world.

 

Unknown to Xavier, Magneto has located Trask Industries and the Sentinel prototypes set to be unvieled at the White House, and has filled the Sentinel chasis with metal.

 

In Washington, Xavier, Logan and Beast arrive at the White House to seek out and stop Raven. Meanwhile, Magneto arrives in epic fashion, raising RFK Stadium and dropping it around the White House, enclosing the President, Trask, and his cabinet. His arrival activates the Sentinels, now under his control. Controlling the Sentinels, Magneto uses them to attack the crowd. The President and Trask flee into the secure bunker underneath the White House, which Mystique has infiltrated alongside them, posed as a Secret Service agent. Logan and Beast must now fight through Sentinels to stop Magneto, who makes a televised speech that humans are right to fear mutants. Logan is able to break away, while Beast focuses on the Sentinel, and rushes to confront Magneto. Magneto sends metal chunks of the stadium at him, until impaling him with rubar from behind. The rubar entangled in his body gives Magneto control over Wolverine, and magnetically hurls him off into the Patomac River.

 

While all of this is going on, the Sentinels have located the X-Men in 2023. Magneto, Storm, Bishop, Colossus, Blink, Warpath, and Sunspot all fight against the Sentinels, putting up as much resistance as they possibly can before all being killed off one by one. Magneto is the only one to escape, retreating back into the temple, hunkering down with Xavier, Kitty, and Iceman, all watching over Logan as he drowns in the future alongside his body in the past.

 

In the past, Magneto is able to use his power to rip the secure bunker from underneath the White House, and bring it right out to the White House lawn. Disguised as the President, Mystique confronts Magneto, telling him to shoot her (as the President) to send his message, but to spare everyone else. Mystique only wants the death of one man - Trask - she doesn't want the war that Magneto is intent on bringing. Magneto refuses, but is distracted by a Sentinel who has identified him as a mutant and began to engage him. Magneto uses the metal he implanted into the Sentinel to rip it to pieces, before being shot in the neck by Mystique. Now with the upper hand, she targets Trask once and for all.

 

Xavier freezes everyone around them and projects himself into Raven's mind, telling her that her actions will have dire consequences. He acknowledges the tight grip and controlling nature he's had over her for years, and finally tells her he has faith in her to make the right decision. Hesitant, she finally puts the gun down.

 

At the same time in the future, the Sentinels, who have killed off all of the X-Men, have now broken into the temple and are bearing down on Xavier, Magneto, Kitty Pryde, and Wolverine. Just as the Sentinels are set to attack, reality disappears and the temple empties. Logan awakens, but not in the temple. Rather, he awakens back in the mansion in the year 2023. As he wanders through the mansion, he sees Iceman, Rogue, Beast, Colossus, Kitty Pryde, and Storm all in the mansion alive. He also encounters Jean Grey and Cyclops, alive and well, a surprise after experiencing the deaths of both of these friends many years ago. He finds Xavier in his office, telling him he needs a little help with history after 1973. Professor X realizes that Logan has awoken back from his time travel in the past, and acknowledges that he and Logan have a lot of catching up to do.

 

In 1973, Logan's body is retrieved from the Patomac River. On the boat is William Stryker, claiming he'll take Logan's body. However, unknown to anyone else on the boat, William Stryker is actually Mystique in disguise.