Doggett continues his investigation of Deputy Director Kersh.
A ship captain delivers a message to Dr. Nordlinger, who upon reading the contents instructs the captain to return the vintage World War ll merchant marine craft to its base.
Follmer leaves the reclamation plant when he sees no sign of Doggett. Shannon McMahon has held him underwater but passes air into his lungs to help him breathe.
Doggett regains consciousness at his house to find McMahon there. She tells him she is a bioengineered soldier and that Knowle Rohrer was part of the same programme. Doggett thinks Rohrer is dead but she tells him that his kind cannot be killed.
Meanwhile Rohrer approaches the captain aboard the ship and informs him that he is the new second in command. He quizzes the captain about the vessel's mission. Later, the body of the original younger officer is found in the water.
Reyes, Doggett and McMahon meet with Scully. McMahon tells her that the US government has changed the molecular structure of chloramine to breed a generation of super soldiers. She is a Stage One prototype.
The Lone Gunmen break into the X-Files office after Reyes requests their help. As they access a phone system, they happen upon someone dialing Carl Wormus' phone number. The caller turns out to be the captain, warning that the FBI must be contacted so the lab aboard his ship can be exposed. Rohrer is nearby, eavesdropping. The call is traced to a phone booth.
The Captain gets the jump on a Navy SEAL guarding the lab aboard the ship. He orders Nordlinger to hand over every scrap of data on the project. He doesn't see Rohrer creeping up behind him.
Doggett, Scully and Reyes arrive at the phone booth to find Rohrer. Doggett tries to shoot him but bullets don't work. As Rohrer is about to kill him, McMahon appears and decapitates him. Rohrer's headless body rises and stabs McMahon with its arm. They both fall into the water.
Scully discovers an electronic filing system on board the boat. She realises the scientists were manipulating human ova in the lab for transplantation. Doggett finds a bomb and urges them to leave. They take cover as the ship explodes.
Deep beneath the water, Shannon McMahon's eyes suddenly pop open. And later, after Scully tucks William in for the night, the child's mobile begins to turn, seemingly by itself.