Logan is in Bristol on the West Coast of England, screaming Jean's name, who has been missing since last night. He is using the faint psi-link that he and Jean have to find her, but up until now he has had no luck. He finally finds her at the checkpoint carrying two children through the weapons detector the Eurasian Army has set up to process all the humans that the Sentinels have now saved from America. Thousands of humans are surrounding the two mutants with hundreds of Sentinels still dropping off more. Jean walks to an older man sitting at a desk, who has the torrential task of processing most of these humans into Eurasia. As Logan screams Jean's name, the older man tells a youth who is standing in front of him that he has passed and he will be able to be relocated thanks to the Displaced Human Act.
Logan catches up to Jean and they both passionately hug. As they embrace, three people appearing to be just more refugees talk. One of them tells a man named Pierce that he recognizes the mutant as Weapon X. Pierce chides the man and, calling them Clegg and Slocum, asks if they were stupid enough to be carrying any tags (weapons). Another says they are clean and the three remain walking towards the weapons scanner. Still in conversation, Logan asks Jean why she is so against the bombing raid against Apocalypse?
Nearby, at scanner number three, a soldier detects a man carrying a concealed weapon through. Unknown to the soldier, the man is really a mutant named Box; and he is the weapon. Pierce, Clegg, and Slocum watch on and they all recognize the mutant. They suspect that he was most likely was sent as a divergence, to allow them to slip through the gates unnoticed. Both Box and his accomplice Copycat, remove their disguises and attack the Eurasian Soldiers and surrounding bystanders.
Where Jean stands, she hears the plasma bullets and she begins to have flashbacks of a time where she was in the pens, and the soldiers there were using the pen's rejects as target practice. Using her psi-link with Logan, she doesn't have to say anything but the feeling both are now possessed with can be summarized with one word: "KILL!" Seconds later, Weapon X slashes through Box, stabbing him in the chest, easily killing him. Jean reaches towards Logan as his back is turned, she asks him to stop because their battle is over. "Over?" Logan questions. He next asks her if she is going to try to save the mutants in America or is she going to stick by his side for him? Logan walks away from Jean, giving her no time to answer his question, just time to think about their relationship and if saving America means sacrificing their happiness together.
In one of the lead airships stationed above London, Logan walks to meet with the Human High Council to brief them on the perfect targets for them to attack in America. As he walks, Mariko Yashida runs to catch up with him and she calls out his name. He stops to turn and sees her as she asks to speak to him in private. As they walk into an empty room, she reminds him of the time they knew each other in Japan, when she was only a teenager. She also asks him to not call her Lady Mariko, but what he used to call her; Mari. She explains that she wanted to talk to him because she does not trust Brian Braddock. He seems to have way too much concern about the war between humans and mutants. Logan just explains it away by pointing out that Braddock Industries manufactures all of the Sentinels the Trasks have created. As they continue to talk about what could have been between them and current affairs with the council, an explosion happens right underneath them on a different airship.
On a video screen, the captain of the blimp being attacked radios a mayday signal to the blimp that Logan is on, pleading for help because he is being attacked by mutant terrorists. He tells the lead blimp with Logan on it that his own ship is on a direct course to the airship that contains the Analog Guidance System for the Doomsday Attack. Lady Mariko asks Weapon X to do something and as he runs off to jump out the window, he instinctively calls her Mari. As he falls from the window, he hopes he doesn't burn up in the flames before he gets to the other blimp. He also wonders why he called Mariko Mari and if it really just slipped from his heart.
In the airship Logan just jumped from, Mariko runs into the control room and sees Brian Braddock and Moira Trask talking. Moira speaks of how they must save the guidance system, even if it means sacrificing themselves. Brain says that he is not willing to sacrifice himself or the others because he feels the world needs them alive. Emma screams for a concentration of laser blasts on the ship and Mariko interrupts saying that Logan is down there.
Pierce stands in front of his two cronies as Clegg talks about holding the only two soldiers still alive on the airship. Pierce sends his cyborg arms stabbing into the two soldiers, killing them and leaving no one else alive left on the airship. Or so he thinks, as Logan busts through the ceiling and into the room. Pierce sends the other two cyborgs to stop him. Logan easily takes out the two cyborgs and as the airship begins to fall, it takes out the ship with the Doomsday system on it. As they fall to their apparent deaths, Logan heads to finish the job earlier and take out Pierce.
On the airship holding the High Council, they watch as the other airship crash-lands and burns. All are shocked when they expected no one to walk from the fire but instead see Logan, still burning, walking out. What saved him was his psi-link with Jean. As he burned, he thought he might die; but something brought him back. It was Jean's voice in his head telling him "Goodbye"!
On an airstrip in Cornwall, Jean is in an old propeller airplane, leaving for America. Logan is driving hard to catch up with her on a Motorcycle and as he nears the plane, he begs her to stop. He cannot let her leave and warn the mutants in America, because that would jeopardize the mission. After he jumps on the already taking off airplane, Jean kisses him and asks him to kill her quickly for the love that they had one time-shared. Moments later, as she flies away, Jean holds her neck and looks down to see that Logan had jumped off. Logan watches the sky until the plane is just barely visible. In silence, he is both mad at her for the love she had spurned and sad that he will miss her.