The movie starts in West Virginia with a lady (an FBI agent) parking her car into an outdoor garage in a snow encompassed landscape. It then cuts to a man leading a team of FBI agents looking for something into the snow. Here we meet Agent Dakota Whitney (Amanda Peet) and Agent Mosley Drummy (Xzibit). The scenes switch back and forth. The FBI lady's dogs are barking in her house while she is parking her car and she is attacked by two men but she scars one of the men with a garden tool before being kidnapped. Cut back to the man leading the FBI agents through the snow as he eventually stops and says it's here. The agents find a severed arm in the snow with scratch marks that match the garden tool that was used.
Cut to Dana Scully speaking before a group of doctors at a Catholic hospital about a boy that has a rare condition. She speaks with another doctor over a video conference and clearly is smarter then her as Scully already has all the answers. As she leaves, Drummy speaks with Scully and tells her that the FBI needs to get a hold of Fox Mulder. She tells them that she does not know where he is and no longer works with him. He only asks that she tries.
Scully drives up to a remote house and walks into a private office where Mulder is seen clipping a news article and posting it on to a wall. She tells him that the FBI needs his help and he starts to do the Mulder ramble. After some talking we see Mulder has grown a beard and tells her that he does not want to help since he is a wanted man by the FBI. Scully tells him they are going to overlook the past. He says no and Scully closes the door. He sees a picture of his sister on the door and decides to help on one condition, they fly in a helicopter to DC.
Scully and Mulder show up at the FBI offices where they meet Drummy and Whitney and are briefed about the case. Drummy wants nothing to do with the paranormal, but Whitney believes in it and in Mulder.
They then go to the house of where the man that lead the FBI earlier lives. The man is Father Joe (Billy Connolly) and he called the FBI and told them he had vision of a women. Turns out, Father Joe lives in a dormitory area for convicted pedophiles. He molested 37 alter boys. Scully has some words with Father Joe because of her religious beliefs. Father Joe leads them to the crime scene but Drummy accidently turns into the wrong driveway. Father Joe feels something and goes to the correct crime scene. They don't find anything there. Drummy feels he is wasting their time. Father Joe walks around the area and stops and says this is where she was taken from. He falls to his knees and starts to cry tears of blood.
Back at the hospital, Father Ybarra who is in charge, talks to Scully about transferring the boy (from Scully's earlier lecture) to a hospice where he can die in peace since they only want to help the curable. Mulder finds Scully and tells her about the tears of blood. Scully does not believe Father Joe. Mulder ask Scully for her help some more.
We then see Scully lying in bed deeply thinking and Mulder is lying next to her. She believes that she can help the sick boy and Mulder refers to their son William. Scully mentions that the severed arm had traces of an animal tranquilizer.
We then see a women swimming in a public pool and a man in the pool with her. She leaves the pool and he is sitting in his snow plowing truck already. He pulls away and she gets into her car. She catches up to him later on the snowy road. He crashes into her side and she veers off the road and crashes into something and is knocked out. She is then kidnapped.
Scully and Mulder and the rest of the FBI are looking in the snow again because Father Joe had another vision. Father Joe mentions dirty glass. Drummy wants to finish searching because it is late and resources are depleted. Mulder believes in Father Joe and continues to search. Father Joe walks some more and then stops and tells them that it is here. They find a head frozen in the snow. Father Joe tells Scully to not give up.
Mulder is back at Quantico and finds out that inside of the ice were a dozen body parts all cut up and that they must have found were the serial killer was dumping the body parts. Scully urges Mulder to give up and let the FBI handle the case now. Mulder does not want to stop and we see there is turmoil in their relationship. Scully is faced with her own battles with the sick boy at the hospital and Mulder feeling an urge to keep going on.
Back in the hospital Father Ybarra has decided to move the sick boy to another facility. Scully disagrees and tells the panel that there is a cure using stem cells. They move forward with the operation and Scully is seen in her office printing searches of stem cell research off of Google.
The FBI find the car that was crashed off the road and Father Joe tells them that he doesn't feel anything. Just as they are about to leave Mulder sees a medical bracelet in the snow and remembers seeing a picture of the missing agent with the same type of medical ID bracelet. They look in the car and find a bathing suit. They then go to the local pool and find out that the missing girl and the missing agent both swam there.
Mulder tells Scully they are close now but Scully does not want to hear about it anymore and that she cannot go down that dark place anymore. The FBI have figured out that the man was targeting people on their rare blood type, AB-.
Scully stops at Father Joe's place and demands to know why he told her to not give up. They argue about religion and he quotes scripture, Proverbs 25:2 (It is the glory of God to conceal a thing: but the honour of kings is to search out a matter). Father Joe then goes into convulsions.
We then see an operating room where a liver is being taken out. The kidnapper is there to pick the organ but is stopped by the Richmond PD. He is questioned but gets released.
We then cut between scenes of Scully operating on the sick boy, and the girl that was kidnapped in some type of cage in some building somewhere. She tries to escape but gets attacked by dogs.
Cut back to the FBI serving a warrant to the organ transplant company. Just as they are searching, the kidnapper shows up but runs away. Whitney and Mulder chase him after he drops his organ transplant bag. He runs into a construction site and they lose him. Whitney says she saw him but it is too late, he pushes her off the ledge and she falls to her death. Drummy opens the bag and sees the head of the missing FBI agent.
Back at the hospital we see Father Joe recovering, Scully tells Mulder that he is a very sick man and is dying of lung cancer. The FBI have suspects, the man that kidnapped the girls and his boss who owns the organ transplant company. Father Joe does not recognize them until Scully mentions you know him from when he was a boy. Turns out the boss was one of the 37 alter boys that he molested. Mulder needs to test Father Joe and ask if he thinks that the FBI agent is still alive, he says yes.
Mulder needs to continue and find the other girl. He believes that she is still alive while Scully is confronted with the parents of the sick boy. They say they don't want to continue with the stem cell treatments. The mother tells her you don't know what it's like to be a mother. She convinces them to continue the treatments.
Mulder then goes into Nutter's Feed and ask for the animal tranquilizer. The man tells him that you need a prescription. Mulder then notices the snow plow truck pull up and hides. The Russian kidnapper needs more drugs. Mulder decides to follow him. Scully notices something while doing her stem cell research. Russians were able to detach the heads of dogs and attach them onto other dogs to keep them alive for weeks. Mulder is run off the road and over a cliff by the truck. Scully tries to get a hold of Mulder but cannot, she calls Drummy but he is of no help and tells her she will find someone that has more balls.
The kidnapper's truck breaks down and he continues to walk the rest of the way. We then see them operating on the boss. He has scars on his face from the garden tool that the FBI agent used on him. He also has the arm of a female attached to him to replace the one that the FBI found in the beginning of the movie. They prepare the kidnapped girl for surgery. The Russian doctors want to take his head off and put it on the girl's body to keep him alive.
Mulder crawls out of his car and walks to the abandoned snow plow and finds a hammer. Tow trucks find Scully's car and pull it up. The police tell Scully you must know someone high up, enter AD Walter Skinner (Mitch Pileggi).
Mulder finds the complex where the surgery is being conducted. He is attacked by a two headed dog but kills the dog. The kidnapper looks for him but Mulder find his way into the building. We see the head fully detached and even for a moment fully aware of what's going on. Mulder is tranquilized and dragged outside.
Scully and Skinner are driving around looking for Mulder, they pass some mailboxes and Scully tells Skinner to stop. She sees a mailbox 25 2 (the biblical verse). She looks through its contents and sees an invoice from a medical company. They get silent and hear dogs.
Just as Mulder is about to get hacked into body parts, Scully knocks the kidnapper out. Skinner goes inside and locks all the doctors up. Scully saves the girl and Mulder and Skinner have a moment.
Mulder is then back in his office clipping the newspaper article. It says that Father Joe was an accomplice. Mulder does not want to believe that. He says that he will clear his name by finding out the time that he died and that it should match the same time that the boss died. Mulder asks what Father Joe told Scully and she tells him. She then has a hard time deciding if continuing the treatment is right or not and tells him that she wants to leave and go somewhere else after this. Mulder and Scully kiss and she finishes her operation on the sick boy.
The credits roll and after the credits we see Mulder and Scully on a row boat in the middle of paradise.
