Scully, searching for Mulder in his apartment, encounters the benevolent Navaho elder, Albert Hostin. He says she must find Mulder, "for the sake of us all."
The Smoking Man drives Mulder to a pleasant suburban house. Tells him it's his "new life." Of course, he says before walking off, you're free to go back to Scully and the X-Files, but why not take a look around?
Back at the hospital, Scully and a security officer review videotapes that go black at the very moment Mulder was taken out. But Scully sees that Mulder's mom was talking to someone, and she thinks she knows who that was.
Mulder enters "his" house. The pantry is filled with his favorite instant foods. Deep Throat, the shadowy informant whom Mulder had thought dead, emerges and the two men hug. The now jovial Deep Throat advises Mulder to enjoy his new life.
Afternoons in Utopia
Mulder sleeps. He walks the bright beach and sees the boy, whose sand castle has crumbled. Mulder says, "That's OK, buddy. You can build it again. Just start again."
Agent Diana Fowley arrives in Mulder's new bedroom, wearing a long evening gown. She murmurs sweet nothings and they kiss.
Scully is trying to reach Mulder's mom, but keeps getting the answering machine. A clerk drops off an interoffice memo envelope. She opens it and finds a translation of the mysterious saucer wreckage inscriptions she's been studying as part of an expensively-printed guide to Native American mythology.
Since it tells of the "Apocalypse" and the "Sixth Extinction," Scully knows this is big. She calls Skinner and asks if he sent this material which, she raves, foretells mass extinction and the "myth of the man who can save us."
He repeats that he doesn't want to be involved and hangs up, so she goes to see him, only to find him slumped over his desk, unconscious. A long-haired vagrant type flees the office, but Scully is unable to capture him.
Morning at the suburban house. Mulder has spent the night with Fowley. She's talking about having children.
Back in the Georgetown area, Scully enters Kritschgau's apartment, quite angry, and accuses him of orchestrating the attack on Skinner.
When she notices that he's hacked into her computer files and (he says) forwarded the "advanced genetic" information from the saucer to the National Institutes of Health to prove Mulder is "biologically alien," she deletes the files and stalks out.
A beautiful day in the neighborhood
Mulder and Fowley go to visit the Cigarette Smoking Man, who apparently lives near them in the suburbs. CSM answers the door. He's got a bigger house, he explains, because he has more "mouths to feed" -- grandchildren and Mulder's long-lost sister, Samantha.
Mulder turns and Samantha is there. She welcomes him with a big smile.
Unfortunately, Mulder is actually lying unconscious on a big metal slab with CSM and Fowley are standing over him. Fowley asks CSM if the comatose Mulder dreams. "I'm sure he dreams," the chain-smoker says.
Later, Scully confronts Fowley in a hallway at FBI headquarters, says she "smells cigarette smoke" on her. Angrily, she tells Fowley to think of how Mulder once was so promising and full of life, but Fowley coolly replies with, "I'm always thinking."
The Cigarette Smoking Man meanwhile gloats with a scientist, delighted to finally have a "fully realized hybrid" in the person of Mulder. However, the scientist notes that Mulder "may not survive the procedure," even though CSM calls that a "hero's fate."
Mulder's dreams flit from one scene to another. A wedding. A funeral. CSM's reassuring hand on his shoulder.
Fowley visits Mulder on the slab, seemingly upset by the fact that they did not give Mulder a choice in the matter. CSM says Mulder is getting a chance "to become the thing he always sought."
Mulder's dreams flash by. He is now an old man, and he finally knows that the beach kid wants some help building a big flying saucer made of sand.
Visions of fire
Albert Hostin visits Scully again to tell her she's not looking for Mulder in the "right place." He points toward her chest. She interprets this as a call to prayer.
Back at the slab, Fowley tells CSM the genetic procedure could kill his son. CSM retorts that this procedure, by "forcing the next step in evolution," is humanity's only hope for survival. Lab workers tinker with Mulder, whose eyes won't close. Fowley walks off in distress.
Mulder dreams he's an old man visited at bedside by CSM, who hasn't aged a day. Mulder wants the window shades open, but CSM tells him he "should be at peace." All of Mulder's friends and allies are now dead, the chain smoker says.
The fading Mulder murmurs that "we're the last, you and I." A smiling CSM says "The end and the beginning," and sanguinely says there's "nothing to be done."
He goes to the window for a smoke, and looks out over an inferno. Spaceships are swooping down, and the city is being annihilated.
In the real world
FBI Assistant Director Skinner, who's had an unusually tough time of late, is unconscious on the floor of his office while the nefarious Krycek, who implanted the nano-probes in Skinner in the first place, burns the saucer inscription translation.
Scully wakes up to find an envelope slid under her door containing a magnetic-stripe card with an official-looking eagle insignia.
While lab workers prod Mulder, Scully rushes down a hallway, using the card to enter the slab room.
Mulder is happy to see her, but since he's still wearing the old man makeup, this must be a dream. She accuses him of being a traitor, deserter and coward, but he refuses to look out the window, saying he's tired. She tells him to get up and fight.
The real Scully has also entered the lab, where she finds Mulder unconscious and unattended on the slab. The Smoking Man and all the scientists are gone. She insists he wake up. He opens his eyes and gives her a weak smile.
A week later, Scully visits Mulder at his apartment. His head is bandaged beneath a baseball cap, but he seems to be doing pretty well. He says Albert Hostin's dead and had been comatose for two weeks, despite his apparent recent visits.
Scully says Diana Fowley's been murdered and, while the two women had never been close, it was Fowley who helped save Mulder by sending the book and hallway key.
Mulder tells Scully she was his "constant," his "touchstone," during his recent bad times, and she says he was the same for her. She kisses him on the forehead, then leaves with a smile.
And on the beach, Mulder and the boy have completed a sprawling spaceship of sand, seen in aerial view.
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