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This is very disjointed, and very stream-of-consciousness, but here goes:

Mulder and Scully had quit the FBI, or were run out on a rail, whichevia.

At the beginning of the movie, we see an attack against a woman at her residence in West Virginia. She turns out to be an FBI agent.

A supposedly psychic ex-Priest has visions related to this now-missing female FBI agent. The FBI recruits Scully from her job in a Catholic hospital, so that she in turn can recruit Mulder, who has gone "underground."

The Priest leads the FBI to severed arms in West Virginia, citing "visions." The Priest says the missing FBI agent is still alive, so the FBI believes it is in a race against time to find her. The FBI wants Mulder to assist because he has experience with psychic phenomena. The Priest has a dark past as a child molester, and lives in a facility where many convicted molesters live in a dormitory setting. Scully resents him from the time they meet, and makes her resentment known. Mulder wants to believe.

The disappearance of the FBI agent is discovered to be part of a larger crime ring, where the villain (a Russian immigrant) harvests organs for an experimental medical research facility in West Virginia. On the operating table in this facility for much of the movie is one of the Priest's former molestees, who is now a very sickly looking adult in need of organ transplants, and who (as Xzibit's character Special Agent Drummy puts it) "is married in Massachusetts" to the villain. When the FBI discovers the Priest's connection, agents immediately believe the Priest to be an accomplice. Scully again confronts the Priest, and he goes into a seizure.

The subplot throughout the movie is Dr. Scully's battle against Catholic hospital administrators, who want to declare her young male patient beyond medical help due to a rare disorder with no known cure. Scully wants to try an experimental treatment. The Priest tells her, "Don't give up." Scully convinces the boy's parents to try an experimental therapy. The subplot eventually merges into the main plot.

While researching stem cell therapies for the boy, Scully happens upon an internet article about a Russian research facility which just happened to be doing experiments which match the organ harvesting going on in West Virginia. She adds 1 and 1, and tries to reach Mulder to let him know what's she's found, but he's not answering his cell phone. Scully fears the worst. The FBI agent in charge (Xzibit's character) blows her off; he had declared the case "closed" when it discovered the severed head of the female FBI agent. Gross! But Scully doesn't give up. She enlists the aid of their old FBI boss Walter Skinner. Scully and Skinner head to West Virginia, and find the car Mulder was driving, crashed and abandoned.

With the Priest on his deathbed at Scully's hospital, Scully uses a scripture passage the Priest gave her during one of their disagreements to find and save Mulder, who accidentally happened upon the research facility. Scully saves the villain's last victim in the middle of a Frankenstein-like operation to save the dying former molestee. Ewwww!

The last scene in the credits is an animated scene of Mulder rowing a boat in the middle of the ocean, with Scully in the boat; the animated Mulder and Scully look up at us, and wave.