Mulder and Scully are back together again but in dangerous circumstances while Skinner must bargain with the Cigarette-Smoking Man to spare the agents their lives.

Scully and Skinner remain at gunpoint but suddenly the door crashes open and in runs Mulder who also has his gun drawn. This leaves Skinner with no choice but to put down his weapon but explains that he won't hand the digital tape over that he is carrying because it is the "only way we've got to bring these men to justice".

Meanwhile, Scully's mother goes to the hospital where Melissa is in an induced coma. Elsewhere, Mulder and Scully meet with the Lone Gunmen to show them a picture taken in the 1970s containing Mulder's father along with Deep Throat, the Cigarette-Smoking Man and a man who is identified as Victor Klemper by Langly who turns out to be a Nazi scientist who was allowed to escape to the US to contain his experiments under an operation codenamed Paper Clip. Suddenly, Frohike enters telling Scully about the condition her sister is in.

Meantime, the Cigarette-Smoking Man is questioned by the Well-Manicured Man among other men about the terrible mistake that his assassins did in killing the wrong woman. They also demand that they have the digital tape in their hands but the Cancer Man cooly replies that he'll have it for them in the morning.

Mulder and Scully visit Klemper who directs them to a mining company in West Virginia, all their answers will be found there. Straight after the agents leave, he quickly calls the Well-Manicured Man to tell him that Mulder is alive. Mulder knows that they are all in danger so calls Albert Hosteen to carry a message to Scully's mother telling her that her daughter can't be there to comfort her dying sister.

Skinner decides that the only way to give back Mulder and Scully's safety is to arrange a deal with the Cigarette-Smoking Man, he would be willing to hand over the digital tape in exchange for the agent's safety. Cancer Man doesn't want to hear any of it and simply replies, "I don't work deals".

The agents go to the mining camp as instructed where they discover a secret tunnel filled with secret medical files including those of Scully and Mulder's sister. The only thing is that Samantha's file had originally been Mulder's. Just as he realizes this, the lights go out, Mulder runs off to see what is happening and Scully is left on her own. Suddenly she witnesses what look like aliens run past her as she struggles for her flashlight. Mulder, meanwhile, rushes outside only to see a huge spacecraft hovering over the mining complex. When it disappears, several armed men arrive in cars and start searching the place. The agents manage to escape despite continuous gunfire.

Having arranged a meeting with Skinner in a local cafe, Skinner tells them about the deal he is willing to make. Mulder says that he would rather find out what is on the tape to find out what happened to his sister and his partner. "Is that answer worth your lives?" Skinner replies. In the end, they accept to making the trade after Scully tells Mulder that the truth is no good if they're dead.

Skinner makes a surprise visit to the hospital where Melissa is staying but soon ends up chasing a mysterious man who is hovering around the room where she is in. He enters a stairwell but is beaten up by Krycek and the same man that killed Melissa who end up running off with the digital tape that they came for. Soon after, Krycek almost gets killed himself when the car he is sitting in blows up just as he gets out and realizes that his accomplishes mean to kill him for the fatal mistake he made.

Mulder and Scully return to see Klemper but instead meet with the Well-Manicured Man who tells them that Klemper is dead. He starts to explain all to them. He says that after the Roswell crash in 1947, Nazi scientists were transported to the US to try to create an alien/human hybrid. Genetic data from millions of humans was collected through smallpox vaccinations and Mulder's father, who threatened to expose the project was kept silent about Samantha's abduction. Meanwhile, Krycek calls the Cigarette-Smoking Man and tells him that's he still alive and still possesses the tape that he is looking for. This obviously means that the deal with Skinner is off.

Mulder, needing information after what he has been told, goes to see his mother to ask her whether his father was made to make a choice between Samantha being abducted or himself. She reluctantly replies, "It was father's choice, and I hated him for it. Even in his grave I hate him still."

The Cigarette-Smoking Man meets with Skinner but explains that there can't be any deal because there isn't a deal to make. Skinner does have one last trick up his sleeve and brings out Albert Hosteen to meet him. He explains to him that if any harm comes to either of the agents, Albert is prepared to recite everything that was on the digital tape having memorized it all. He has also told 28 other native Navajo people so the Cancer Man would have to kill them all to conceal the truth.

Mulder goes to see Scully where she tells him that Melissa died. Mulder says that they've both lost so much, but he still believes that the truth is out there and can be found by continuing with his work on the X-Files. "I've heard the truth," Scully says, "Now what I want are the answers."