The agents race against the clock to find a subway killer...
An undercover transit office is tracking a fare evader on the Boston Subway. The officer gets in to an empty carriage, having told his colleagues about the evader through a hidden microphone. The connecting door between carriages opens, and the evader enters. As the officer reaches for his gun the train stops suddenly, losing power. White light fills the carriage, the officer cries out, and the evader runs off through the tunnel. When the officer's body is found, it is missing hunks of flesh.
Deputy chief Karras and Lieutenant Bianco of the Boston Transit Police meet Scully and Doggett - and tell the agents they have eleven hours before the next rush hour to solve the case. The agents are piqued, but Bianco insists no chemical or biological agents were found, so the case is just a single cop killer.
The group is joined by a pathologist, Dr Hellura Lyle, and Steve Melnick, who supervised the building of the tunnel four years previously. Scully decides to monitor the investigation by fiber optic link from the control room, and Doggett sets off into the tunnel with Melnick, Lyle and Bianco.
Melnick cries out in pain - he�s been burnt on the neck. Lyle takes samples of water from the tunnel, in case there is a contaminated seepage - Scully analyses it to find it is just seawater. The group see a running figure, and follow to a fork in the tunnel, where Doggett decides to invesigate the abandoned branch. Suddenly a charging figure collides with Doggett - it�s the fare evader, but now his body is decaying on the tunnel floor.
The party finds three plastic-wrapped corpses nearby, but Lyle sees another running figure. Despite Scully's orders to leave the corpses, they lose the figure - then Melnick screams as a strange sparkling light tears chunks of flesh from his arms. Dogget douses him with water, neutralising the phenomenon, and heads off with Bianco to find the figure. Turning off his torch, Doggett notices that Bianco is luminescing. Bianco tries to run off, so Doggett pulls his gun and orders him to drop his weapon. Bianco does, but attacks Doggett.
A 'hazmed' team rescue Lyle and Melnick from the tunnel, but Scully notices a second team removing the wrapped corpses. Karras must have known the bodies were there all along. Kai Bowe, a marine biologist, approaches Scully with information about a medusa - a jellyfish like sea creature. The organic composition fooled the analysis of the seawater samples.
Dogget regains conciousness to find he is glowing, too. He tells Scully that Bianco must be found to stop the pathogen spreading, but Karras has reopened the subway to commuters. Doggett finds Bianco and tries to carry him to safety, but encounters a small urchin-like boy. He isn�t glowing - his sweat doesn't contain the substance which has been acting as a chemical-electrical conductor in the case of adults.
Doggett finds a leaking crack in the ceiling, but a train is coming with more people who could be infected. He shorts out the third rail with his assault rifle - electicity arcs through the tunnel as the train passes. As the tunnel darkens again, Doggett realises he is no longer glowing.
The organism is destroyed by the electric arc, which means that Karras can�t be prosecuted - the evidence is gone.