A sick young boy is awakened at night by a storm and a bright light. He watches in awe as figures walk out of the light.

Scully finds a copy of the Goochland Guardian newspaper on her doorstep. An article about the young boy is on the front page. Although his family had refused medical treatment for him because of their beliefs, the boy had miraculously been cured. At the office, Mulder receives an anonymous email from someone at the Defense Advanced Research Projects Agency about the same incident. Someone is insistent that they investigate the case. Mulder goes to DARPA, while Scully visits the boy.

The McPeck family is grateful for their son's miracle cure. The boy tells Scully he saw "angels" who looked like men, and one of them pinched his neck. Scully sees that he has a mark similar to her own implant scar. The Cigarette-Smoking Man waits outside the McPeck home in Scully's car. He claims that he was responsible for saving the boy's life, as well as hers. He questions why she is not curious about his technology since he went to considerable trouble to prove his intentions. Scully is not swayed in her distrust. The CSM admits that he is dying, but hopes to pass his knowledge and power onto her. This knowledge includes the cure for cancer. He chose her because he has grown tired of Mulder's stubbornness. He leaves his card with the warning that one word to Mulder will rescind the offer.

Scully traces the phone number on CSM's card and finds the address. It is a large, unmarked office building. The security guard demands her ID, and sends her to an office where the door's nameplate reads "Spender, C.G.B." As if expecting her, the CSM cordially welcomes her in. He tries once again to appeal to Scully. He is dying of a cerebral inflammation caused by brain surgery and wants to leave a legacy. To retrieve the cure for cancer, they must take a trip. Intrigued, Scully agrees. She leaves a message on Mulder's answering machine, saying that she will be out of town for a family emergency. The CSM watches her pack when Mulder phones back. Although she ignores Mulder's call, she manages to discreetly conceal a small microphone in her bra.

The mood in the car is tense, but Scully drives CSM to an undisclosed location. She protests when he begins to light a cigarette, and he agrees to quit smoking in order to gain her trust. He then directs her to the home of Marjorie Butters, a sprightly, energetic older woman. Scully is shocked to hear that Marjorie is actually 118 years old, and that the CSM is the reason for her overcoming cancer. He comments that a miracle such as Marjorie must be the reason Scully became a doctor.

Worried about Scully, Mulder questions her building manager. The man says that she left with a man who smoked cigarettes, and Mulder immediately makes the connection. Skinner tells Mulder that Scully requisitioned a fleet sedan, but there have been no gas charges to track her whereabouts. Mulder is concerned because Scully's mother knew nothing about a supposed family emergency. Suddenly, Skinner's private phone line rings. It is Scully, who asks her boss to relay to Mulder that she is okay. When Skinner offers to let her speak to Mulder herself, she refuses. Mulder is even more convinced that she is in danger.

When CSM and Scully stop at a gas station, she speaks frantically into her hidden microphone, asking Mulder to comprehend what she's recorded. She drops the tape into a mailbox and gets back in the car with CSM. As they drive away from the station, it is revealed that the Black-Haired Man (last seen in "The X-Files" feature film) has followed the pair. He reaches into the mailbox and pulls out the envelope she attempted to mail Mulder.

Late that evening, CSM pulls up to a lakeside cabin. With black leather gloves, he reaches for the sleeping Scully. The next morning, Scully wakes in the cabin. She's been changed into pajamas, and she quickly reaches for the microphone still taped to her chest. Scully accuses the CSM of drugging her, but he humbly says that she was tired and delirious when he put her to bed. He even admits to dressing her in the dark. Scully is determined to leave, but when the CSM tells her she has always been free to go, she hesitates. From a distance, the Black-Haired Man watches the exchange in the cabin.

Meanwhile, Byers, Frohike and Langly show Mulder the emails they uncovered on Scully's computer from a "Cobra" at the Department of Defense. They suspect she had been hiding this correspondence from him, but Mulder does not believe their theory. He and the Lone Gunmen inform Skinner that someone hacked into her computer to arrange a meeting between Cobra and Scully.

The CSM brings Scully a dress for a dinner meeting with their contact. She hides her revulsion for the man and is somewhat alarmed to see that the low-cut dress can not accommodate her hidden microphone. At the restaurant, CSM tells Scully that he involved her because Cobra was skittish about his research falling into the wrong hands. He then confesses that he has not been forthcoming with all the facts about this secret research. Not only is it a cure for cancer, but a cure for all human disease. Its origin is extraterrestrial. Excusing himself, CSM heads outside for a cigarette. The Black-Haired Man approaches him. Troubled, the CSM reports to him that Cobra has not shown. Scully, alone at the table, discovers a note under her plate. It reads "Calico Cove. First light of day."

At sunrise, CSM instructs Scully to take a small motorboat from the dock. She speeds away to meet Cobra. Scully cuts the engine and sits idle in the middle of the inlet. Another boat approaches and parks alongside her. The man driving the boat is Cobra, and he speaks to her as if they had been corresponding for a while. He hands her a black computer disk. Scully tells Cobra that they have never corresponded before and then asks about the information on the disk. This unsettles Cobra, but before he can speak a gunshot rings out. The Black-Haired Man shoots Cobra out of the boat and sets his sight on Scully. She scrambles to restart the boat, but another shot fires. This time the CSM kills the Black-Haired Man with a pistol at point blank range. Scully returns to the dock, furious, and hands the disk to the CSM. He hesitates, and then gives it back to Scully. She takes it and storms off.

An angry Mulder is silent to Scully while the Lone Gunmen check the disk. It is completely blank.

She takes Mulder back to the building of CSM's office. It has been vacated. Mulder says that the CSM used her, but can not figure out why she is still alive. Scully is incredulous, believing that the CSM had told her the truth. She questions why the CSM would use her to save himself at the expense of the human race.

At the cabin, the CSM stands on the dock, holding the disk. He contemplates it for a second, tosses it into the water, and then lights up a cigarette.