This episode opens with a voiceover by Mrs. Scully and beautiful images of Dana's childhood. We hear a story about her, as a tomboy, shooting a garter snake with a BB gun because her brothers were doing it. When the snake began to bleed, however, Dana became very upset. She told her mother that there was something missing from the snake. As the voiceover ends, the peaceful music fades and Mrs. Scully comes into view, sitting in a hard plastic chair in a waiting room. Mulder is sitting beside her, listening to the story. He brings her out of the reverie, saying, "It's too soon, Mrs. Scully. We can't give up." They both look up as another person enters the room. He's carrying something covered in tissue paper, which he sets carefully down on the counter. Mulder and Mrs. Scully approach and look down at it as the man removes the tissue paper to reveal a stone tablet - a grave marker that reads, "Dana Katherine Scully, 1964-1994. Loving Daughter and Friend" and a Bible quotation. Mulder reads the tablet, jaw clenched, and then turns away, shaking his head as if he refuses to believe it.
Mulder's desk is cluttered with Scully's X-file, and there he is in the dark, on the couch watching something questionable on tv. The phone rings.
Northeast Georgetown Medical Center
As the scene changes, we watch Mulder walking quickly down the hospital corridor. His face is lit with intensity and impatience. He breaks into a jog, charging past a nurse who attempts to restrain him and pushing into the intensive care unit. There, attached to indescribable machines and life support systems, lies Scully. Mulder wordlessly comes to her side, and then looks to Mrs. Scully who is sitting mutely by her daughter's bed. He turns, barely suppressed rage written into his expression. He begins demanding answers from the nurses and the doctors, "How did she GET here?!" He loses his control, fighting with security guards as he screams at the doctor to answer his questions, threatening to "do anything!" if he finds out the doctor is working for "them." The scene ends and we fade into a hospital room, an edgy Mulder on one side, sitting beside Mrs. Scully - and the doctor on the other. The doctor proceeds to tell them they have no idea how Scully got there, what's wrong with her, why she's in a coma, and how to get her out. The one thing they do know - she's signed a living will specifying that she does not want to live in this condition. This is no surprise to Mulder, who was the signing witness on the document. He buries his face in his hands.
Returning to Scully's bedside, Mulder finds Melissa holding a crystal over her sister's stomach. "I've been told not to call you Fox," she says cryptically. Mulder seems to find it difficult to believe that Melissa can communicate with Scully while she's in a comatose state, and she insists that he hold his hand over Scully's body. The scene changes and we see Scully sitting in a small canoe, tied by a single rope to a dock. The water is calm and serene, and Mulder and Melissa are standing on the dock, silently looking out onto the water and the canoe. They are surrounded by deep forest. Scully watches calmly as Mulder says, "She's not here." Back in the hospital room, he breaks away impatiently and says that he needs to be doing something "beside waving his hands in the air." He goes home and attempts to contact X. He waits all night, but to no avail.
Back at the hospital, we watch as Frohike comes awkwardly into the room dressed in his finest tux and bearing flowers. Mulder is there to show him to Scully's side, where Frohike spots some irregularities on her medical charts. The scene fades out and we next see Mulder slumped into a chair with The Lone Gunmen. There, they find that there are byproducts of "branched DNA" in Scully's blood - very advanced technology that could act as a high-tech identity card. But the DNA is not active, it's waste product. After a pause, Mulder asks quietly, "Will she live?" There is a long pause as the Lone Gunmen exchange awkward glances. Then they tell him, sadly, that her immune system has been decimated and not even a healthy body would be able to fight off the toxicity of the branched DNA. "Mulder, there's nothing you can do." It won't be the last time he hears that. Mulder's expression is determinedly blank as he stares at the information on the computer screen.
Meanwhile, Scully rests in the canoe and listens to a Nurse Owens who promises to take care of her but tells her that her time has not yet come. As she kisses Scully's forehead, Mulder walks in and mutely stares down at his partner with a woebegone expression on his face. A nurse pushes past him to take some of Scully's blood - but just as the vial is filled and put down, another patient goes into heart failure. Mulder, momentarily distracted, glances away and then looks back - Scully's blood is gone! He realizes that there was a man in a suit standing behind him who has also disappeared, so he checks the hallway and sees the man striding quickly away.
Mulder to the rescue! He sets off at a run, chasing the man into the parking garage. There, he is stopped by X - who is pointing a gun to his head. They exchange heated words, with Mulder's eyes flashing furiously at X. "You ignore my call for help and then you expect me to do what you say - you go to hell!" X insists that Mulder stop chasing the man, but refuses to explain why. "You're MY tool. You got him killed, you got her killed, that's not going to happen to me!" Still furious, Mulder says that Scully's still alive. "I owe her more than just sitting around, doing nothing." He pushes X away and continues chasing the man, all the way into the laundry room. After a few tense minutes of searching in a darkened room, Mulder finds the man and gets him to surrender Scully's blood - but all for naught. X rolls into the room and shoots the guy dead.
Mulder returns to the hospital wing and listens as Mrs. Scully and Melissa consider taking Scully off of the life-sustaining machines, pacing with frustration. The doctor dismisses Mulder's offer of a "branched DNA" diagnosis, and Melissa speaks about the unnaturalness of keeping a person alive against their will. Bowing his head in desperation-sparked anger, he mutters that her opinion is very politically correct. Mrs. Scully lays down the law and says that she will respect Dana's final wish. Mulder looks to the ceiling as if asking for help, then silently shakes his head at her offer that he join them for the "event." Left alone in the waiting room, he stares after them with a haunted expression. What can he possibly do?
And on the lake, Nurse Owens watches as the rope keeping Dana's boat leashed to the dock snaps suddenly, releasing her out into the open waters.
In Skinner's office, the Cigarette Smoking Man puts a file on Skinner's desk and tells him that the contents are true and that if Skinner is having trouble controlling Mulder, "they" would have no trouble. He moves to light a cigarette, but Skinner points to the "Thank You For Not Smoking" sign on his desk. CSM lights up anyway and leaves the room by an alternate door. A few seconds pass and there's a knock at the main door. Mulder strides in, looking worse for the wear, unshaven, and exhausted. He seats himself down and waits. Skinner asks him about the report about the man who was executed in the laundry room. Mulder is flippant, denying everything, and answering his questions with questions. When Skinner gets angry, Mulder asks him how he feels in the face of constant denial and questions instead of answers. He pushes on, insisting that CSM is behind it all and that if only he could find where the SOB lived...
"Oh you can have it all! You can have my badge, you can have the X-Files. Just tell me where he is," he presses on, almost desperately. Skinner refuses to listen, reminding Mulder that they are not the Mafia but the Department of Justice. "THAT'S what I want," Mulder interrupts. But Skinner goes on to say he liked Scully and respected her, but she knew the dangers inherent with the job as they all do. She accepted the risk when she accepted the job.
Mulder starts to leave, but thinks of something - something that has obviously been bothering him the entire time. "What if I... I knew the potential consequences but I.... I never told her?" he asks, though his expression shows that he already knows the truth. Skinner sighs. "Then you are as much to blame for her condition as the Cancerman," he says coldly. Mulder's face doesn't change, and he leaves the room quickly without looking back.
Scully's body, dressed in white and bathed in a pure white light, is laid out on an antique table in an empty corridor. Her father walks up, dressed in uniform. He speaks to her, telling her he loves her and would give anything to spend another minute with her. But her time is not come yet. He walks away, and Nurse Owens is speaking to her now. "I know death is at arm's reach. But Dana, your time is not over."
In the hospital cafeteria, Melissa is eating a donut and looking compassionately down on Mulder, who is bent over his coffee cup in utter despair. First she tries to reason with him, telling him that he could spend the rest of his life trying to get revenge and finding the people responsible, but it won't bring Scully back. He hears her, but he doesn't seem to be listening. His expression is one of defeat and self-hate and helplessness. She tries to make him feel better, telling him that no matter what, whoever has done this to her "has an equal horror coming to them."
He nods his head slowly and then asks, "Including myself?" Before she can answer, a stranger walks up to them and asks for change for the cigarette machine. Mulder says he doesn't have any, and Melissa asks, "What do you mean, yourself?" And again, before Mulder can answer - the stranger returns and tells him that there is a pack of cigarettes already in the machine - Morleys - and walks away. Suddenly alert, Mulder goes to the machine and pulls out the pack of Morleys. Inside is an address - the CSM's address.
CSM is sitting in a sad little hole of a room, with a sad little tv playing some war movie. You'd think with all the atrocities he has to commit, he would get paid enough to afford a nicer place. He hears something and moves quickly for his gun, but not quickly enough. Mulder shoves him violently back into the chair, points his gun at CSM's forehead and shouts that it's his turn to ask questions this time. His voice breaking from care and strain, he demands to know why "they" took Scully instead of him. CSM plays it very cool, expressing disappointment that Mulder is becoming a "player" and losing his dignity, and reminding Mulder that by killing him, he would never find out the Truth. During the very intense discussion, Mulder fights an enormous internal struggle. He comes to the very brink, his finger pressing on the trigger... but he pulls himself back at the last moment.
In his office, Mulder types out a letter of resignation. Shoulders hunched, gaze aimless, he signs his name at the bottom of the form. The scene cuts away and reveals Mulder packing up his belongings into boxes. The basement office looks bare. The door opens to reveal Skinner. Mulder looks like he has been expecting this visit. Skinner has come to rip up the letter of resignation. Mulder says he hates who he's become, he's come all this way only to lose himself.. and Scully. Skinner gives Mulder a pep talk about faith and belief, and he talks about a near-death experience, where he hovered above his body and watched as events unfolded, all the time in a peaceful forest. As he leaves, Mulder realizes that Skinner is the one who provided him with CSM's address.
As Mulder takes a box of his stuff to the car, X startles him in the corridor. The men responsible for kidnapping Scully will be at Mulder's apartment tonight. There, Mulder should be ready to defend himself with terminal force. Everyone is falling over themselves to give Mulder the opportunity to kill. Hearing this offer, Mulder closes his eyes and accepts the information quietly, as if acknowledging that he cannot fight the rush of events. There will be no justice for these men, X insists, unless Mulder takes it into his own hands. And for Scully, Mulder is willing to do that. Time passes. A gun sits in the moonlight on a desktop. Mulder is sitting in the dark, his face covered in shadows - both internal and external, waiting. Just waiting. He hears footsteps and grabs the gun, ready. A knock sounds at the door. And then a voice. It's Melissa. He opens the door just enough for his upper body, and ignoring her for the moment, he peers tensely down the hallway, looking for the men. Melissa asks if she can come in, but Mulder only looks down at her with impatience and irritation. When he says nothing, she looks offended and asks again, "For a second?" Edgy and tense, Mulder steps back and lets her into the darkened apartment. She glances around and asks why it's so dark in there. "Because the lights aren't on," he says tonelessly. She tries to get through to him, telling him that Scully is weakening and that he should go to the hospital. He brushes her off, saying he can't. Offended, she leans in and tells him coldly, "Listen. I don't have to be psychic to see that you're in a very dark place." Mulder shifts his weight impatiently and is barely listening. "Much darker than where my sister is. Willingly walking deeper into darkness cannot help her at all. Only the light--" His nervous fidgeting explodes into an outburst, telling her to cut the harmonic conversions crap. This only makes her angrier, telling him to drop the paranoid cynicism. "Why is it so much easier for you to run around trying to get even, then just expressing to her how you feel? I expect more from you. Dana expects more," she berates him and leaves. He barely lets her get through the door before slamming it shut and mechanically returning to his chair. Reaching behind him, he finds the gun and puts it back on the desktop - glinting in the cold, blue-gray light of the moon.
The scene cuts away, and there lies Scully. Most of the machines have been put away, and she only has a few tubes in place. Mulder enters the room and sits down beside her. Inexpressible sadness on his face. Reaching for her hand, he says, "I feel, Scully, that you believe you're not ready to go. And you've always had the strength of your beliefs. I don't know if my being here.. will help bring you back, but I'm here." He settles back in his chair as if to wait it out. Sad music plays, and the camera moves away. When Mulder returns to his apartment the next morning, it is completely ransacked and overturned. Defeated, he trudges in and leans against the wall, staring at the wreckage. He can't take it anymore. Head bowing slowly, he starts to cry. Sliding down to the floor, he holds his hands out as if to ask, "What, now, can I do?"
Scully lies on a bed in the middle of a peaceful forest. Birds are chirping, and slowly a hospital chair appears beside her bed. And then more pieces of the hospital start to appear, and a nurse walks in. She stops. "Call Dr. Daly!" A closer shot of Scully reveals that her eyes have opened. Back at Mulder's apartment, he is sitting quietly on the floor in the middle of the mess, just staring into space. The phone rings, and he doesn't stir. It seems he's going to let it ring, but when the answering machine picks up, he sighs in exasperation and picks up the phone. "I'm here." As he listens, his face changes from utter bleakness into complete relief.
Next scene, Mulder opens the door to a hospital room. Seeing Scully awake in bed, he smiles widely and asks how she's doing. He's brought her a present - Superstars of the Superbowls. She jokes that she knew there was a reason to live. He holds her hand briefly and tells her to get some rest, and that he just came by to see her and say hi. As he's leaving, she tells him that she had the strength of his beliefs. He nods. Then, reaching into his pocket, he brings out the cross necklace he's been holding for her. Scully and Mulder share a look - gratitude, relief, happiness - and he leaves. Later, alone in her room, Scully asks the attending nurse if she could speak to Nurse Owens. The attending nurse tells her that she's worked here for ten years and there was never a Nurse Owens. As the camera fades out, Scully is left to wonder if Nurse Owens was a figment of her imagination or...