“Medusa” is episode twelve of season eight of The X-Files.
One man is waiting on the underground platform of Clay Street Station in Boston. Another joins and is watching him. The first uses a mic to call in a possible fare jumper and describes the second. The train arrives, the man, Officer Philbrick, calls in an all-clear. The train pulls off and the second man comes in from another carriage. Philbrick is drawing his gun when the train suddenly breaks and he drops it. The second approaches and then there are screams and what look like lightning inside the carriage. The train pulls into another station and passengers get on; Philbrick is missing most of the flesh from his face.
Scully and Doggett arrive at the transit operations centre to be greeted by Deputy Chief Karras and Lieutenant Bianco. Karras thinks they’re late, doesn’t care that Scully wanted to examine the body and wants to know when the line will be clear. The afternoon rush starts in five hours and the line will be back in operation at 4PM. He disagrees with Scully when she says he can’t do that. Scully says the tunnel cannot be reopened. Bianco says the facts are clear; they have a cop killer who is still at large. Doggett asks what the killer used. Scully’s examination of the victim didn’t reveal anything and they need to cultivate the tissue. Karras says the CDC has found nothing. Bianco insists they’re looking for a single man; Karras that the subway will open at 4PM.
On a platform, they’re introduced to the chief structural engineer, Melnick, and Dr Lyle from the CDC. Scully says she isn’t going in; she’s more effective analysing the situation from outside. She wants Doggett to be her eyes and ears, giving him a headset with camera and microphone.
Scully and Karras are in the transit control centre. The third rail is shut down and Doggett, Bianco, Lyle and Melnick head into the tunnels. It’s hot because ventilation was shut down. Doggett wonders why if they’re only after a man. Lyle walks over a water filled pothole, that glows briefly after they pass. Then Melnick gets a burn on his neck from water. Scully wants a sample of the water in the pothole; Lyle takes one and sends the data to Scully. It’s just seawater, but Scully wants a molecular analysis.
Someone is glimpsed in the tunnel and they find an entrance to an old tunnel that’s been shut down for years. Despite Karras claiming it will waste time, Doggett leads the others in. Lyle spots someone rushing at Doggett. It’s the supposed cop killer and he’s also had his flesh eaten away. Bianco says they caught the guy who killed his officer; case solved. In flashes from Lyle’s camera, Melnick sees something. Three bodies, wrapped in plastic, all with flesh eaten away. Scully thinks they might have a contagion after all. Possibly a terror weapon.
Someone is glimpsed outside the abandoned tunnel. They run on and are gone when the others get out. Scully gets in a shouting match with Karras; she wants Doggett to go after the other. They may be infected or causing the infection. Either way, they could cause more deaths. Bianco and Karras insist they have found their man. Which is a truly idiotic statement.
Scully wants to know what’s causing the deaths before any more occur. Karras is bound and determined to open the subway to passengers on time, so that no-one complains. The fact that doing so might well kill the potential complainers is seemingly irrelevant. He and Bianco couldn’t be less helpful if they tried.