En Ami In Goochland, Virginia, the McPeck family drives home in car with an eleven year old boy in back seat. Their car runs a gauntlet of people who are shouting and holding signs. The boy, Jason, has cancer and the religious beliefs of the family prevent them from seeking medical help. At night, a storm comes up, a light glows outside the window and Jason sees men in black approach out of the light.
As Scully leaves her apartment she finds a newspaper outside her door - the Goochland newspaper describing Jason's miracle cure. The family claims the cure was by angels. Mulder also got an anonymous e-mail about it. Someone wants them to investigate. While Mulder checks other sources, Scully visits the family. They believe that it was God's work. Jason says the angels looked like men, told him not to be afraid and pinched him hard on the back of the neck. Scully realizes that Jason has a neck wound and possibly has a chip implanted there, just as a chip cured her own cancer. Scully returns to her car to find the Smoking Man waiting for her. He claims to have saved both Jason's and Scully's lives and left the newspaper and the e-mail. He says he is dying himself and wants to bequeath his cure to her. (He's tired of Mulder's mule headedness.) He leaves a paper on the seat as she drives off.
The paper has a phone number. Scully traces the number and gets the address. Going to the building she finds high security but they send her to the third floor where she finds an office labeled "Spender." The Smoking Man awaits her and tells her that as he looks at the sum of his life, most of his work is in ruins. As the darkness descends, he finds that he has no legacy. He is dying of cerebral inflammation resulting from his brain surgery and has only a few months. He is willing to give her the chips that provide the miracle cure, but she has to travel with him - it will take a few days. She is reluctant, but her interest overcomes her and she leaves word for Mulder that she will be out of town for a few days, claiming a family emergency. She is carrying a microphone, hidden in her bra. Scully and the Smoking Man talk as they drive. He has always had a sort of affection for her and Mulder. He held her life in his hands when he cured her of cancer. The Smoking Man thinks Scully is drawn to powerful men but also keeps distant from them, which is why she would die for Mulder but won't allow herself to love him. She dismisses his comments as "pop psychology." He takes her down a dirt road, and we see that they are being followed. They arrive at a pleasant country home where a woman named Marjorie Butters lives, who the Smoking Man claims is 118 years old, although she is as vital as a much younger woman. She is gardening and greets CSM with a hug. Scully sees that Marjorie has a scar on the back of her neck - apparent evidence of the validity of the Smoking Man's claims for his science. Scully's apartment manager tells Mulder about Scully leaving with a "driver," who Mulder recognizes as the Smoking Man. Skinner and Mulder are concerned but can't find Scully. She took an FBI vehicle and her mother knows nothing about an emergency. Scully phones Skinner and says everything is OK, but she won't talk directly to Mulder. Mulder becomes convinces that she is in trouble. Scully and the Smoking Man stop for gas and she goes to the bathroom, talking on the tape to Mulder. She secretly mails the tape to Mulder but as they drive off the man following them is seen to have gotten the envelope out of the mailbox.
They end up at a lake home, late at night. Scully is asleep in the car and CSM puts on gloves, brushing a lock of hair out of her face. Scully wakes up to find herself in satin pajamas. She thinks the Smoking Man drugged her but he says he just carried her in so that she would be comfortable. They are in Milford, Pennsylvania. She is upset and ready to leave, but finally decides she has to know the answers. The Lone Gunmen arrive at Mulder's apartment, in disguise. They got into Scully's apartment and found e-mails on her computer to somebody named "Cobra." Mulder and the Gunmen barge into Skinner's office carrying Scully's laptop. For the last 6 months Cobra has been e-mailing Scully from the department of defense, but she is unaware of it. Somebody has been posing as Scully to win Cobra's trust. Mulder is convinced that the Smoking Man is doing this and Scully's life is in danger. Meanwhile, the Smoking Man tells Scully that they'll be meeting their contact for dinner and provides her an evening dress. At a fancy restaurant, Smoking Man says that their contact, Cobra, is to human genetic science what the nuclear scientists were to war. The Smoking Man says that if Cobra receives assurances, the science he turns over will be not just a cure for cancer but a cure for all human disease. How? From the final frontier - largely extraterrestrial. Theoretically the Smoking Man can be cured but it appears that he doesn't really want to be. He is a lonely man. The Smoking Man goes outside for a smoke. The man who has been following them approaches and points out that Cobra hasn't shown up, so they have to wait, but Scully won't stick around for ever. The Smoking Man tells him, "Just do your damn job.
Cobra, however, has slipped Scully a note about where she should meet him. The Smoking Man lets her take a small motorboat to the Calico Cove inlet, down the lake. Another boat approaches hers. Cobra comments that they are finally meeting and that she is just as she described herself. He hands her a CD-ROM. She denies that they have spoken before - but he is shot and dies before they can say more. The sniper then targets Scully, but the Smoking Man kills him before he can fire at her. She returns to the lake home where the Smoking Man meets her. Because she still believes him, she gives him the CD-ROM but he gives it back. Later, Scully is at Mulder's apartment where the Lone Gunmen help examine the content of the disk. It is empty. They return to the building where Spender's office was, but it is vacant. Mulder says that the Smoking Man used Scully. Marjorie Butters was a fake. Jason has a chip in his neck but the parents probably won't let them examine him. Scully believed the Smoking Man but Mulder thinks he used her to save himself, to get the science on that disk - saving himself at the expense of the human race. Scully says that for a moment she saw something in the Smoking Man's eyes, a longing for something more than power - something he could never have. Realizing what he is doing, the Smoking Man throws the real CD into the lake, apparently dooming himself and keeping the cure for all disease from the human race.
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