In a top secret government facility in New Mexico, the half-man, half-machine villain known as Bastion is being held captive. Bastion had sought to rid the world of the mutant race during Operation: Zero Tolerance. But now, “that which he sought to eradicate is now coming for him”. The horseman named Death.
Meanwhile back at the Institute, Phoenix calls out to Archangel, Cable and Nate Grey. After Professor Xavier has disbanded the X-Men, she had received a distress call from the Mannite named Nina. Cyclops, Wolverine and Phoenix are “all that’s left of the team” and she needed to turn to the people whom she could trust for help, the men who are nearest and dearest to her.
Phoenix awaits anxiously with Cyclops and Wolverine for Archangel, Cable and Nate to arrive. After they gather, Cyclops and Phoenix give them a quick run down of the situation. Cable tries to set aside his issues with Wolverine, and Nate with the X-Men, to work together as a team.
As the team homes in on their destination, Cyclops discovers that it is the base of Operation: Zero Tolerance. He tries not to let his emotions get the better of him, especially after what Bastion had done to him. When they land, they tread cautiously upon the barren landscape. Phoenix scans the area and finally picks up some brain activity from inside the facility.
The team infiltrates the facility and finds Nina and the Mannites. Phoenix senses more brain activity, but Nina warns her about venturing further into the facility. The team ventures in and finds Bastion, or what’s left of him. Nina is terrified. Bastion warns them about Death, who is after the Mannites. Phoenix urges Nina to take them to her friends quickly so they can get away from Death as soon as possible.
With her powers, Nina melts through a titanium door to her friends beyond. Death is hot on their heels and starts to slice through the doors. Nate attempts to hold Death back while the rest try to figures a way out of the facility. Cyclops still intends to go back for Bastion and one of the Mannites projects a schematic of the facility, providing Cyclops and Cable another way to and back. Phoenix and the others stay behind to help the Mannites.
Seeing as there’s no escape, the Mannite named Grace activates a computer failsafe. Phoenix immediately sends a telepathic message calling Cyclops and Cable back to regroup before the whole facility explodes. But Cyclops insists that he and Cable are approaching Bastion and they’ll find their own way out.
Phoenix tells Nina to use her teleporting powers to get them to safely. Nina succeeds in getting them back to the Blackbird, but the other Mannites refuse to follow. Nina tells Phoenix that they went “somewhere else”. With no time to spare, Phoenix gets everyone into the Blackbird.
Cyclops and Cable arrive to find Bastion gone. They have no time to find a way out, so both men have to force their way out. Reaching the evacuation tunnel, Cyclops discovers that the pods are missing. Cable telekinetically forces them up and out, and makes it out in time and into the Blackbird before the facility explodes.
Phoenix worries about the fate of the Mannites who have disappeared, and about Death, who’s identity is still a mystery.