Mulder storms in the hospital asking for Scully's whereabouts and becomes very upset and anger when he doesn't get an answer. When a nurse tells him that she is in intensive care, Skinner, accompanied by other FBI agents, arrives. Mulder ignores Skinner and he follows him and demands answers as to why he is alive. But Mulder doesn't respond and keeps looking for Scully. When he enters ICU and finds her, he is clearly shocked to see her hooked up to a ventilator in bed. He asks Skinner what happened to her and Skinner says she just lost a lot of blood and is dying. Skinner wants Mulder to go with him but he refuses. He wants to stay there by Scully's side. Skinner takes his arm but Mulder pulls away angrily and as Mulder struggles to escape, the other FBI agents take him under control and take him away.
At Chief Blevins' FBI office, Mulder is escorted in and Skinner is present. Blevins tells him that now that he is alive the investigation will take another course and offers him a chance to help himself. Mulder asks how is that. Blevins wants more information but Mulder doesn't understand how that will help him. Blevins reminds Mulder that Scully lied to them and asks him who is protecting whom. Mulder is silent and asks if he's done. He leaves but Skinner intercepts him outside. He tells Mulder he needs a buddy and says that he's been withholding forensic evidence about the body found in his apartment. He was the one keeping the secret. Mulder wants to know how he can help him, Skinner wants to know why Scully lied for him. Mulder tells him about Scully's disease and how it was given to her by a mole inside the FBI but Mulder hasn't identified him yet. Skinner reminds Mulder who his real friends are.
At a racetrack, the Elder, accompanied by a silent man is watching a televised hearing in the ethics of human cloning when the Cancer Man arrives. The Elder tells him that Mulder is alive. When the Cancer Man says he cannot be underestimated, the Elder tells him that Mulder is free because of him. Cancer Man doesn't deny this. The Elder reminds him that their FBI man is exposed and the project is at risk but Cancer Man sees it in a different way, saying that what Mulder saw is good for their plans; he's also in trouble and he needs their help. In exchange of what? "Loyalty to us", Cancer Man replies and adds that Mulder is more valuable alive than dead. When he leaves, the Elder tells the silent man that he can proceed now.
Back at the hospital, Mulder visits Scully and he's happy she's improved a little. He sits on her bed, takes her hand and kisses it. He tells her that he will testify to everything he knows about the FBI -Defense Department conspiracy but Scully says that if he does that, Skinner will reveal the forensic evidence. Scully is sure Skinner can't be trusted but Mulder doesn't believe it and insists that the evidence will expose the conspiracy. Scully says that if he's not sure they'll bury him, but Mulder thinks that if he doesn't testify they'll begin to bury the truth. Then Scully, squeezing Mulder's hand, tells him that he should tell them she was the one who killed that man but Mulder refuses. Scully then says that he can and asks him to at least give her some meaning to what happened to her. Mulder doesn't agree. Scully's mother and brother enter the room and notice them holding hands. Mulder greets her, kisses Scully good-bye and leaves. On his way out, Bill and Mulder introduce themselves and Bill asks Mulder to put work aside and let Scully die with dignity, then he goes into Scully's room. Mulder is confused.
In a stairwell of a parking structure, we see the silent man entering and carrying a suitcase. When he opens it, we see a disassembled sniper's rifle.
As Mulder leaves the hospital, he runs into the Cancer Man. He says that he's there to pay him some respect for his cleverness and what he has done for Scully, breaching into the security Defense Department facility and finding the cure for her disease. Mulder says what he found was useless but the Cancer Man thinks otherwise.
At the Lone Gunmen's lair, Mulder pours the last drops of ionized water of the vial he retrieved from the DD facility and a tiny microchip comes out. He thinks this might be the cure for Scully's cancer and tells them the story about Scully's chip on her neck and the result of its removal.
Michael Kritschgau is being questioned by the FBI investigative committee. Kristchgau confesses that he gave Mulder and Scully classified information shortly after Ostelhoff died. The reason? A government conspiracy against American people. There's a minor commotion in the members of the committee. Then he's asked if he knows who killed Ostelhoff, but he doesn't know. When asked if there's any connection between that death and Mulder and Scully, he says he knows about one connection: his son's, who died in the morning. Kristchgau says that he works for the Defense Department but part of his remuneration comes from a congressional lobbying firm called Roush. Skinner asks what that is but he has no idea. Blevins and another agent exchange looks.
Back at the hospital, Mulder is trying to convince Scully's mother and brother that implanting that chip on her is worth the try. Bill Scully thinks it's crazy and Mulder and him argue. Bill accuses Mulder of not being a doctor and he has no place for suggestions. Mulder asks the doctor if she will have to stop her conventional treatment. The doctor says at that point all he has left is quite unconventional. Scully is looking at the vial in her hands and she says that she will give it a try and that her mother and Bill don't know all the facts.
The silent man is assembling the rifle and loading it.
In the corridor outside Scully's room. Mulder is sitting there alone. When Bill steps out, he sees him and stops. He asks Mulder is he believes that crap. Mulder says what crap. Bill shakes his head and says that Scully is his big defender and she doesn't want to disappoint him. But Mulder doesn't care. If the chip works, he doesn't care what Bill thinks Scully thinks about him. When Mulder tells Bill that he is not part of the tragedy family, Bill accuses him of being the reason for it and that he's lost a sister and he's about to lose another one. He also asks him if he's found what he's looking for. After a pause, Mulder says no. But he adds that he has lost his sister and his father for the things he's been looking for. Bill asks if they are little aliens. But Mulder says he doesn't know anymore. Before leaving, Bill tells Mulder he's a sorry son of a...
Mulder's cell phone rings. It's the Cancer Man and he wants to know how Scully is doing and if he found the chip. Mulder says yes. The Cancer Man wants to know if he still has to earn his trust despite the gesture. After saying yes, the Cancer Man tells Mulder he's arranged a meeting. At a small diner that night, Mulder is sitting at the counter, when a car arrives. It's the Cancer Man... and a grown-up Samantha Mulder. Mulder leaves and walks to the car and Samantha approaches him and with tears in her eyes she tells him she was afraid she was never going to see him again. Then she adds that he always told her something had happened to him that night. Mulder is confused and asks who. Samantha says "my father", meaning the Cancer Man, who is still sitting behind the wheel. She says that she doesn't remember what happened and all she did was try to forget. She was told she was an orphan and then her foster parents told her she was going to meet her father. She was told it had all been a secret and he and her mother hadn't told anyone to protect the family. Mulder can't believe this. But he can help her remember. Samantha doesn't want to and came to see him because her father told her he wanted to see her so badly. Mulder tries to talk Samantha out of it but she refuses to believe him. When Mulder tells her to come with him and see their mother, Samantha is surprised that she is still alive. But she won't come, she has now a life and children of her own. Mulder begs her to stay but she stands up, leaves the diner and meets the Cancer Man in the car. They drive away.
At the hospital, Dr. Zuckerman continues Scully's treatment. He tells her that if she's making any progress, it will show on the PET scan. Scully asks the doctor if he's holding his breath. The doctor tells her that he's treating her cancer as aggressively as he can, but Scully knows the type of cancer has very poor response to treatment. Then she asks him if he's ever witnessed a miracle. He hasn't. He has witnessed some people make recoveries but he can't dare call them miracles.
Mulder is walking on a sidewalk while the silent man is watching, aiming outward and downward. When Mulder stops, he is joined by the Cancer Man and they walk together. Mulder asks what he wants from him because he has given him all these things, things he's ever wanted. The Cancer Man knows it's true, that no act is completely selfless. But he hasn't come to ask, he's come to offer him the truth he's so desperately sought, about the project and the conspiracy. Mulder tells him that he has seen the truth, but the Cancer Man tells him that he has only seen a part of the whole. Then he tells him that Kristchgau can tell him the real story about extraterrestrial life. In exchange for what? Mulder asks. The Cancer Man says to quit the FBI and come work for him. Mulder says no deal. The Cancer Man smiles and when he starts saying that after all he's given him, Mulder interrupts him angrily and accuses him of giving him nothing. But The Cancer Man wants something from him. But Mulder doesn't give in. The Cancer Man leaves knowing that Mulder has a hearing the next day to testify for the murder of Ostelhoff.
At the hospital, Scully's mother visits her and she questions her faith, asking her mother why she wears the cross around her neck. But her mother assures her she hasn't lost her faith. Scully regrets pushing Father McCue away. Then she tells her mother that she's not getting any better, that the PET scan doesn't show any improvement. They hug, but her mother tells her that even when she's afraid of telling her, she has to tell someone. Scully asks her mother to call Father McCue.
At the Syndicate headquarters, the Elder is watching the congressional hearing. As the camera pans the audience, it spots Skinner talking to another man. The Elder grabs the phone to make a call. He tells the person on the other line to turn on the television and watch the hearing. Whatever the person tells him, The Elder is not satisfied. He says that their colleague was supposed to fix the FBI problem and demands him to fix it immediately.
At the hospital late at night, Scully is asleep in her room. Mulder enters quietly and watches her for a moment. He looks confused and he debates whether to wake her up or not. Finally, he kneels next to her bed and lays his head on her bed and cries silently.
Mulder enters Chief Blevins' office the next day looking depressed and expressionless. He tells Mulder that he has forensic evidence indicating that he was the one who shot Ostelhoff. Mulder asks how he got it. But Blevins won't tell him unless Mulder points out someone else as the murderer. Mulder is silent. He then asks him if he is ready to testify that he was not the man who fired that shot. Mulder asks why he's there. When Blevins tells Mulder the man he shot worked for the Defense Department, Mulder replies he was spying on him but he doesn't know for whom. Blevins then tells him that Scully was ready to name the man involved in the plot against them and that they believe she was about to name Skinner, but Mulder doesn't believe that. When Mulder asks Blevins to show him evidence that Skinner is the man, he refuses and instead offers Mulder to exonerate him from murder if he names Skinner as the traitor. Mulder stands up and leaves.
Later that day, Mulder visits Scully at the hospital, who looks tired and drawn. He tells him that he was there the night before and wanted to discuss something with her. He says that he was offered a deal that could've saved his life and he was willing to take it. But after what happened in the morning, he won't take it. When Scully asks him what happened that morning, Mulder tells her about his meeting with Blevins. Scully asks if he will name Skinner. Mulder says no and Scully knows they will prosecute him. Mulder tells Scully that they have evidence that he shot that man but Scully wants Mulder to blame it on her. But Mulder refuses to do so... because of her mother, because of her brother and because he could not live with it. Then Scully asks Mulder if he had already made up his mind, why come see her? Mulder says he came to her because if he was making a mistake she would talk him out if it. She takes his hand. The door opens. It's Father McCue. Scully tells Mulder he'll be in his prayers. Mulder kisses her good-bye and leaves.
Mulder arrives at the FBI where everyone is waiting for him. Blevins begins accusing Mulder of lying on his report, for killing a man passing him for his own body, but Mulder interrupts him and says he'd like to set the record straight and name the guilty ones. Skinner wants a short adjournment but Mulder ignores him. Mulder begins his testimony reminding everyone about his assignment, being paired up with Agent Scully, believing she was sent to spy on him and how she didn't follow their orders because of her integrity as an investigator. Blevins says that Scully lied to them about his death, but Mulder says she lied because he asked her to because he had evidence about a conspiracy.
At the same time, in the parking structure, the silent man is at his post and through his scope he tracks The Cancer Man on the street...
Back in the hearing room, Mulder continues. He talks about experiments being conducted on human beings and that the responsible ones are people within the government...
At the same time, Scully is at the hospital with Father McCue, both praying...
Mulder continues. He tells them about Scully lying in a hospital bed, diagnosed with terminal cancer, because of the same experiment, conducted without her consent and that there are men tying to cover their tracks. Mulder wants to name the author of this conspiracy but an agent interrupts and demands to know if Mulder shot the man in his apartment. Mulder will answer the question after he names the man responsible for Scully's condition, the surveillance in his apartment and who is sitting in the room...
Scully continues praying in the hospital... The Cancer Man is at his apartment, watching a picture of a young Mulder and a young Samantha. Through the window of his apartment, we see the parking structure...
The Agent demands Mulder to answer the question Chief Blevins asked him. But Mulder says he can't do that because Blevins in the man he's about to name. Everyone in the room is shocked.
The Cancer Man, still in his apartment, notices a red dot in his chest. He's alarmed and looks out the window. The silent man pulls the trigger.
Blevins leaves the room as Mulder sits quietly on his chair. He runs to his office. Inside, the Agent from the hearing room is on the phone as Blevins runs inside with a panic look. The Agent turns around, shoots Blevins in the chest and exits.
The Cancer Man lies badly wounded in his apartment. He touches the frame that holds the picture he was watching before. He closes his eyes.
In the hospital, Mulder is sitting outside Scully's room when he sees Skinner approaching. He tells Mulder The Cancer Man is dead. He then hands Mulder the picture The Cancer Man was holding. But Skinner tells him that there was no body found at the scene though there was too much blood for someone to have survived. Skinner wants to know how he knew Blevins was the man. Mulder says he just guessed. Skinner then tells Mulder that Blevins had been on payroll for four years to a biotechnology called Roush and that it's somehow connected to what happened. But Mulder assumes whatever connection there was, it's been erased by now. Skinner agrees and thinks everything has been erased. But Mulder says not everything. Scully's cancer is in remission. Skinner is stunned. Mulder tells him it's the best news he could ever imagine. But Mulder doesn't know what treatment caused the remission. Skinner stands up to see Scully, who's with the doctor, Father McCue, her mother and borther. Mulder stays outside looking at the picture, a family picture. He cries.