In rural West Virginia, a female FBI agent is kidnapped (by a character identified as the First Abductor) from her garage as she arrives home in the evening. She strikes his face with garden tines, but he overcomes her. FBI agents search for her in the snow using rods, led by a snow-covered field. One man, not an agent, runs out in front and eventually kneels and digs in the snow, where a man's severed arm is found.   He is a defrocked pedophile priest, Father Joseph Crissman, who claims to be having visions about the kidnapping.  

FBI Assistant Special Agent in Charge Dakota Whitney approaches Scully at Our Lady of Sorrows, a Catholic hospital where Scully is employed as a physician. Whitney wants Mulder's help with the case of a kidnapped female FBI agent. Scully says she no longer works with Mulder, but Whitney persists in her believe that Scully probably at least knows how to contact Mulder. If Mulder helps, all FBI charges against him will be dropped.

That evening, Scully returns home -- a two story country house. There are out buildings suggesting it was once a farm house. Mulder is inside, busily cutting out newspaper clippings about paranormal phenomenon. Scully tells him about Whitney's offer and he at first declines. But he relents, if Scully will join him. An FBI helicopter picks them up and flies them to Washington where they join a briefing on the missing agent. Scully, of course, is skeptical, and is also revolted by his crimes. Whitney wants Mulder to determine whether these really are visions. Whitney's partner, Agent Mosley Drummy, thinks Father Joe knows the kidnappers.

They go to see Father Joe where he lives, in an apartment complex for sex offenders. He cannot explain his visions and denies any connection to the missing woman. Scully walks outside, disgusted, but Mulder talks her into coming along as they take Crissman to the field where the arm was found. He finds nothing. Scully encourages Mulder to drop it.  

Back at work, Scully is preoccupied by one of her patients, a boy named Christian Fearon, who has a degenerative disease. Conventional therapies cannot help him and the rest of the medical staff thinks there are no alternatives.  

They take Father Joe for a drive in West Virginia, to see if he can identify the location of the kidnapping, which he does.   

A second woman is kidnapped in West Virginia. When she leaves an indoor swimming pool, a man driving a pickup truck with a snow blade on the front (identified as the Second Abductor) follows her and forces her off the road, taking her semi-conscious from her wrecked car. When the agents ask Father Joe, he claims that the second victim is alive, but he cannot tell where. He can also see the first victim, as through a glass darkly. At one point, Father Joe tells Scully, "don't give up. " He also cites Proverbs, 24-2. Scully doesn't understand.

Somehow they get Father Joe out onto a frozen lake. The officials are ready to give up, as is Scully, but Mulder persists, calling back the FBI agents. They end up finding the severed human head of the first victim in the ice. When a massive chunk of the ice is removed and melted, many other body parts are found. This is clearly a serial kidnap and murder case now. Mulder interprets the "through a glass darkly" as looking through the ice.

Mulder gets the FBI to assemble a listing of recent disappearances of women and the team, including Father Joe, soon arrive at the wreck of the second victim, still where it was run off the road. Father Joe gets no feeling from sitting in the car. In the trunk, they find the second victim's swim suit. Near the car, Mulder finds a Medic Alert bracelet in the snow. He remembers seeing a photo of the kidnapped FBI agent and she also wore a Medic Alert bracelet. Mulder asks where the nearest swimming pool is and they go to the building, where the attendant isn't much help. But they eventually determine that both women swam there and both had the same rare blood type. The FBI concludes that it is a black market body organ harvesting ring, and they proceed to investigate in that mode. An autopsy of the FBI agent's remains reveals the presence of a powerful drugs used as a muscle relaxant in animals.

Scully is increasingly disturbed about her patient, Christian. She goes to Father Joe 's apartment, urgently asking why he told her to not give up. Was it about her patient? He has no idea. The words just came to him. As they talk, Father Joe goes into convulsions. Mulder arrives with other authorities as the ambulance prepares to take Father Joe to the hospital. Mulder is surprised that she is there, but she insists that she cannot go back to "the dark" with Mulder. (Note: Fr. Joe ends up at Scully's hospital for treatment, suggesting that Our Lady of Sorrows is located in Richmond, Virginia.)

In her office, Scully Googles stem cell therapy and begins planning a cutting edge surgery with Christian, even though the hospital administration opposes her. About this time we also see a fenced compound in West Virginia where the second victim is locked in a box. The First Abductor is obviously in bad condition under medical care and other people in the background appear to be in an improvised surgical room.  

In another hospital, the Second Abductor picks up a human organ provided in a surgery suite. Police officers there, alerted to the organ harvesting ring, stop him and question him, but he appears to be legitimate, because his employers really is in the human organ business. When word gets back to the FBI, they research him and discover that the man is married in Massachusetts to another man (the First Abductor) who was one of Father Joe's victims, years ago and today suffers from many cancers.  

Scully begins her gene therapy procedure on Christian, inserting a fluid deeply into his brain.  

The FBI gets a search warrant for the business where the Second Abductor works and while they are there, the Second Abductor approaches, but slips away. Mulder and Whitney, however, are outside she see him emerge. They give chase through nighttime city streets, ending up in a building under construction, where they become separates. The Second Abductor pushes Whitney off an open floor and she falls several stories to her death, and he escapes.

Scully and Mulder confront Father Joe with photographs of the two. He is mortified, but this is clearly the connection that has caused the visions. Father Joe sees the visions as a gift from God to allow him to redeem his past offenses. Mulder and Scully argue and Mulder appears to decide to leave Scully, because his search for answers is so important.   

Soon after, Christian's parents tell her that they wish to discontinue the gene therapy on their son, even though they do not know yet is it is working. They have been counseled by a priest who has repeatedly urged Scully to NOT use aggressive treatments, but they say they have decided for themselves. Scully asks, however, what if the therapy were to actually work?  

Mulder goes off on his own, driving in Scully's car through the area where the women were kidnapped .   He inquires at a feed story whether they sell the animal muscle relaxant, and they do, but only with a prescription. The Second Abductor also visits the store, but in a moment of intuition (or maybe recognizing him through a window), Mulder hides from him and follows when the pickup with the blade drives away. The Second Abductor notices Mulder and turns around, using the blade of the pickup to push the car off an embankment. It rolls several times before coming to rest. The Second Abductor drive away, but a hydrolic line on teh snow blade of the truck breaks, dropping the blade to the ground. The Second Abductor leaves the truck and walks back to the fenced compound.

Scully, in her office, notices that her computer printer his paused with a document in memory. When she prints the pages, she finds a report of some Russian research that amputated a dog's head and attached it to another dog's body. Father Joe's mention of hearing dogs in his visions causes Scully to put two and two together. She cannot reach Mulder and phones Agent Drummy. He refers her to the local police to report Mulder is missing. Scully flies into a rage and demands to talk to someone who has the fortitude (not the word she used) to help her.

Mulder painfully crawls from his car and begins walking along the snowy road. At the abandoned pickup, he finds a tire iron and takes it with him for protection. He comes to the fenced compound and enters, but is attacked by a large dog, which he injures critically with the tire iron. The Second Abductor investigates and searches for Mulder. Mulder bursts into the surgery room where the second victim has been drugged and placed into a vat of ice water. The surgeon is doing something to her neck. But Mulder is overcome and, himself, drugged with the muscle relaxant.  

Scully has enlisted the assistant of FBI Assistant Director Walter Skinner, her former boss. They are searching for Mulder and are called to Scully's damaged car. Mulder is nowhere to be found but they find his cell phone, so they know he is on his own. They continue driving. Skinner tells Scully not to worry, that Mulder is obviously OK because he walked away from the car. Mulder won't do anything stupid, Skinner says. Scully just gives him THAT look, and Skinner has second thoughts about his statement. As they drive, Scully shouts to stop. She has seen a rural mailbox with the address of Box 24-2, the citation from the proverb mentioned by Father Joe. She and Skinner get out and hear dogs barking. But from what direction?

The Second Abductor drags Mulder outside to a clopping block which is obviously used to dismember bodies. Mulder is groggy and can hardly focus, but he knows he is in trouble. Just as the Second Abductor prepares to drive the axe into Mulder's chest, Scully strikes him hard with some kind of blunt object and knocks him out. The first thing Mulder says to her, in his groggy condition, it "sorry about your car." Skinner, meanwhile, has entered the surgery room. The First Abductor's head has been removed from his body and is being kept alive by something similar to a heart-lung machine. The doctor has made the first small incisions to remove the head of the Second Victim. Skinner, with his gun, stops them. Scully enters, saying that Mulder is outside, but immediately realizes that she needs to act to save the Second Victim. She turns off the equipment keeping the head of the First Abductor alive. Skinner goes out to Mulder, puts his jacket around him, and holds him to help warm Mulder as he considers how to get the dead weight of Mulder inside.

Back at their rural farm house, Scully is about to leave for work. Father Joe died at the same instant that his former victim, the First Abductor, did. The FBI say he was an accomplice, but Mulder thinks that is unfair. Maybe the visions really were messages from God. Scully is still troubled about whether to continue her gene therapy on Christian. Mulder counsels her that she has to decide what feels right. He says that the two of them could just get out of there. Somewhere where the darkness won't follow, she asks? Mulder doesn't think it works that way. Later, in the hospital, it is clear that Scully is continuing the therapy.

The closing credits of the movie show repeated stylistic scenes of ice, slowly transitioning to scenes of ocean, eventually revealing a rowboat. Mulder is rowing while Scully reclines in a white bikini. They both wave at the camera.