A man waits alone on the Clay Street train platform in Boston. He is an undercover transit cop who, speaking into a microphone on his lapel, describes a gangbanger that has jumped the turnstile. The train arrives, and the cop steps in the empty car as it moves into a tunnel. The gangbanger enters from another car. Suddenly, the train lurches to an abrupt stop and loses its power. Strobes of bright light fill the car, and a man’s scream is heard. The gangbanger jumps down on the tracks and runs off into the tunnel. At the next stop, incoming passengers see the officer’s body on the floor of the car. Huge chunks of his face and body have been eaten away, revealing sections of skull and skeleton.

At the Boston Transit Operations Center, Scully and Doggett talk with Deputy Transit Police Chief Karras, who wants to reopen the line in time for the afternoon rush hour. Scully insists on keeping the train closed until the man’s cause of death can be determined. Armed and wearing a flak jacket, Doggett proceeds into the tunnel, joined by Police Lieutenant Bianco, Center for Disease Control pathogen expert Hellura Lyle and transit engineer Steven Melnick. Scully, manning the expedition from above ground, communicates with Doggett by radio and video camera. As they venture into the tunnel, they find it to be unusually hot because ventilation was shut down. Suddenly, Melnick screams, indicating a burn on his neck. Dr. Lyle does a sample analysis on a puddle that the group had passed, but finds that the liquid is only seawater.

In the darkness, Lt. Bianco sees a figure move. Doggett chases after it into an unused and obsolete tunnel, and gets attacked by a man with horrifyingly decayed features. The man is the gangbanger who previously ran off into the tunnels. Lt. Bianco is ready to end the search when Melnick spots three bodies wrapped in plastic. Dr. Lyle sees a shadow run off, but, upon investigation, the team can’t find anyone. Scully, believing a contagion is still a risk factor, directs them to leave the bodies and continue into the main tunnel. Melnick screams again, this time with burns on his arms and hands. Scully orders them to pour fresh water on Melnick from their canteens. She guesses that they may be facing some kind of bio-chemical agent. While Dr. Lyle stays with Melnick, Doggett and Bianco start into a side tunnel. No one notices Lt. Bianco’s hand glowing faintly green. Scully meets the hazmat team as they bring out Dr. Lyle, the deteriorating Melnick and the three dead victims. She orders that the bodies be taken to the CDC and accuses Karras of hiding dead bodies that he knew were down there.

Doggett and Bianco trudge into the next tunnel. Bianco’s face and hands begin to glow green, but it has no other effect on him. He tries to leave, but Doggett pulls a gun on him. Bianco kicks him in the face, knocking Doggett out, and he escapes. Doggett now has the green fluorescent glow on his skin. Scully, meanwhile, gets a visit from Dr. Kai Bowe, a marine biologist. She has analyzed the water from the tunnel, and has found that it contains a sea creature, called a medusa, which is why the CDC missed it when they inspected the liquid. The medusas glow with bioelectricity, but do not burn people on contact. Something triggers it. Scully fears the worst for her partner.

Doggett wakes up and speaks to Scully on the radio. If he is to stop the spread of the contaminant, he needs to find Lt. Bianco. Karras tells Scully that he has reopened the subway and there are already passengers on the platform. It is now becoming urgent to protect the thousands of passengers. Doggett locates Bianco, lying in the tunnel. Scully tells Doggett to get out, but Bianco begs him to stay. Doggett helps Bianco walk, and they see a child’s shadow. The boy, who is unaffected, points to a wall. Scully figures out that sweat triggers the electricity. Since the boy’s sweat glands aren’t fully developed, he has not been affected. The boy motions Doggett toward a big leak in the ceiling with water running from the bay. He leads him to a main track, where trains from the reopened system are about to cross. Doggett is faced with a train heading towards him. He places Bianco’s gun on the third rail, which triggers a spark when the train hits it. The electricity charges into the puddles of seawater, killing the medusa. It vanishes from Doggett’s and Bianco’s skin.

Doggett is later treated at Boston General Hospital. Scully tells him that he is rid of the organism and is perfectly fine. The boy is with social services. Plastic surgeons are working on Melnick and Bianco, and the three bodies’ deaths are being attributed to an unknown pathogen. Since there is no proof that Karras endangered people’s lives, he can’t be criminally charged for keeping the trains running. He was merely doing his job. Scully congratulates Doggett for saving all those people’s lives. “You figured it out,” he tells her. “I was just your eyes and ears.”