When one man's shadow turns into another man's nightmare, Mulder and Scully must stop it before it kills again but at the cost of a number of lives along the way.
A normal scene at night in a hotel room, an executive suddenly hears some commotion coming from the hallway outside his motel room. Going to the peephole, he sees Dr. Chester Banton, a man claiming that he has killed somebody. When Banton steps away from the door, his shadow suddenly sucks the executive into the floor. Scared, Banton runs off leaving a black patch of energy on the floor.

Scully's old student and friend, Detective Kelly Ryan calls the agents in on the case with the baffling evidence that has been left behind. When Mulder notices the black smudge on the floor only one thought enters his head, spontaneous human combustion.

With not much to go on, the agents go to visit the second victim and find the same smudge on the victim's floor as well as a train ticket in the garbage. It matches the same train station where all the other victims were on the night of their deaths. Ryan orders two police officers to search the station where they encounter Banton but, against the warnings of the scientist, suffer the same fate as the others.

Mulder decides that the only way to catch the guy is to examine weeks of security camera tape from the train station on the nights of the murders. He soon notices Banton, a man sitting in the same place everyday and everyday staring at the floor. Enlarging the picture, they notice a logo on his jacket reading 'Polarity Magnetics', the same place where the first victim worked. Visiting the centre, they meet with Dr. Davey who is surprised to see that Banton is alive, saying that he had been missing for five weeks and that he was involved in a terrible accident at the plant involving a particle accelerator. He had been investigating dark matter but was locked inside the testing room while the machine was in motion which caused him to disappear leaving his shadow burnt into the wall.

Mulder and Scully go back to the train station, their only hope, and Mulder observes that the soft light cast over the ground doesn't cast any shadows. Suddenly, Banton appears but before he can run off the agents corner him. Again Banton warns them that he is a dangerous man and just as Scully is about to step into his shadow, Mulder shoots the lights out.

Taking him to a psychiatric hospital where they interview him, he tells them that his shadow is like a black hole and that it reduces matter into pure energy. The government is after him and they won't stop until they find out what dark matter really is.

Ignoring Mulder and Scully's advice, Ryan plans to move Banton to a county jail but X beats them to it and along with two other men, also plans to transport him. Before he can though, the lights turn on causing Banton's shadow to kill the two men and X, sensing the danger he is in, lets Banton run off, the lights flickering behind him.

Banton runs off to Polarity where he tells Dr. Davey that the dark matter is in him and that they must destroy it before the government get their hands on it. Ryan interrupts him though but Banton has no choice and kills her with his shadow. Davey locks Banton in the chamber just as he wants but finds out that Davey is also with the government and wants to salvage the thing that is in him, he is "lightning in a bottle". X again appears though and shoots Davey before he can alert his bosses. Mulder and Scully are just too late but do witness Banton in the particle chamber disappearing as there is a bright flash. Mulder later contacts X saying that he wants nothing more to do with him but before he leaves X replies, "I didn't kill him" referring to Banton.

Scully attends Ryan's funeral, where Mulder tells her that Davey is missing and that maybe it wasn't Banton in that chamber after all, but Davey. Meanwhile, X approaches a lab scientist. "We'll be studying this man for a long time" as we see Banton hooked up to a machine subjected to a light flashing over and over again as a tear runs down his face.....