In a race against time, Doggett leads a team of professionals into the Boston subway system in search of a murderer. However, Scully discovers that a killer sea organism is responsible and Doggett is infected.
An undercover cop waiting on a subway platform feigns being just another commuter, as a suspected robber appears. They both get onto the train and the police officer draws his gun, as the other man starts to walk towards him from behind. The subway comes to a screeching halt and the policeman drops his gun, which slides away. The robber approaches as screams are heard, flashes of light are seen, and the train loses power there. Later, when the train is running again, a batch of commuters enter the subway car and find the undercover cop, with the flesh on half his face and his left arm stripped down to the bone.
When Agents Scully and Doggett arrive at the operations center for the Boston subway system, they are rudely greeted by Deputy Chief Karras and Lieutenant Bianco of the transit police. They eagerly want the FBI to get the job done fast, since the subway has to be reopened in five hours and Karras is irritated that Scully performed an autopsy on the transit cop. Scully has no idea what killed the man yet, but the CDC has been unable to find any biological or chemical agents in the subway. Bianco believes the suspect used acid or lye to destroy the man.
They are introduced to the rest of the team going below – Structural Engineer Steven Melnick and Dr. Hellura Lyle, from the Pathogens branch of the CDC – but Scully decides it will work better if Doggett acts as her eyes and ears, and she analyzes the situation from up there in the center. She will watch and hear what is happening through the camera and microphone on Doggett's headset. They march into the dark tunnel.
Not long into the tunnels, Melnick gets a burn on the back of his neck, suggesting a chemical leak, but the test of the puddle nearby shows nothing relevant. It is just salt water. Melnick mentions that the tunnels run along the harbor in some places and they get sea water leakage from time to time.
Moving ahead, they find an abandoned section of the subway tunnels. They approach the plastic sheeting that seals off the unused tunnel. Out of the tunnel bursts a man with his ribcage and teeth exposed. He knocks Doggett down. He is the suspected robber, eaten away like the other man. It proves he didn't kill the cop and that there may be a contagion. While Lt. Bianco tries to convince them to leave, since they got the robber, they notice three bodies with the same flesh-eating injuries, wrapped in plastic. It becomes clear that there may be a cover-up of the problem in the subway.
Lyle spots an unknown person running away from them in the subway, so the team realizes they have to go on to find them, much to Karras' irritation.
While approaching the spot where the train lost power, Melnick starts crying out in pain. Visible electrical flashes start destroying the skin and flesh of his left arm. Scully tells Doggett to pour water on it. This stops the flashes. Scully theorizes that it could be some sort of bioweapon and that they need to contain it.
While Lyle stays with badly injured Melnick, Doggett continues onward with Bianco. When Melnick returns to the surface, he seems to be getting worse but Lyle seems okay. Scully then sees the three bodies are being taken away by non-CDC hazmat people. When Scully confronts Karras about this and says the bodies must go to the CDC, Karras tells her that he is organizing it. Scully tells Karras that she already had arranged it and accuses Karras of knowing something was wrong and covering those bodies up. Although Karras claims not knowing about this, he allows Scully to send the bodies to the CDC.
When Doggett notices the green glow of whatever it is on Bianco in a dimly lit former subway station, he refuses to allow the lieutenant to leave. Bianco takes down Doggett and runs away.
Scully meets with Dr. Kai Bowe, marine biologist, about the water sample. She explains that the sample contained microscopic sea creatures called Medusas which are made out of calcium and are bioluminescent. Bowe doesn't know why they can make electricity but Scully realizes it takes time for it to trigger.
Doggett regains consciousness and pursues Bianco. He learns from Scully that Karras has gone ahead of plan and allowed the passengers onto the platforms. The subway will start back up, despite the danger.
When Doggett finds the wounded Bianco, he discovers that his condition has gotten worse and Scully tries to show Karras his condition, but Karras flees the room before Scully can show him. Doggett then carries Bianco on his back and helps him continue through the tunnels.
They encounter a boy down there with no signs of the luminous green substance on him. Scully realizes that sweat is causing the electrochemical reaction, since it is conductive - The boy doesn't have well-developed sweat glands yet, so the medusas don't affect him.
Doggett follows the boy to a major leak from the bay with the green glow on all the walls. The boy seems to have led him there more to show a way out of the tunnels just beyond the leak. Doggett gets Bianco and follows the boy back to the leak point.
The train is coming through the tunnel and Doggett decides to use Bianco's gun to dead short the third rail in order kill the medusas. He doesn't want to let the people on the subway get exposed to it.
Scully comes to see Doggett in the hospital. He is perfectly fine; the Medusas were washed off of him easily before any electrical shocks melted his flesh. He is informed that Bianco and Melnick are with the plastic surgeons, the boy is with social services, and no criminal charges will be pressed against Karras since Doggett's overload of the third rail destroyed the Medusas in the tunnel.
- Although the date is not clearly defined, Doggett once states, "It's the middle of winter." In the same scene, Doctor Hellura Lyle refers to the television programme Survivor II. This series, also known as Survivor: The Australian Outback, first aired from January 28, 2001 to May 3, 2001.
- With the full-time return of David Duchovny to the main cast in the following episode "Per Manum", the opening credits that were introduced in the episode "Patience" featuring only Gillian Anderson and Robert Patrick make their final appearance.
Cast and Characters
- Vyto Ruginis as Lt. Bianco
- Penny Johnson as Dr. Hellura Lyle
- Brent Sexton as Steven Melnick
- Judith Scott as Dr. Kai Bowe
- Adam Gordon as Officer Philbrick
- Bill Jacobson as Thug
- Ken Jenkins as Deputy Chief Karras