PART 2 OF 2
A naval captain on a vintage World War II Merchant marine vessel passes through a sequence of tight security checkpoints. He approaches a door that hides a science lab where cells are being manipulated. Dr. Nordlinger opens the door to receive the Captain’s communiqué, but he is somewhat unsettled by the note’s request. The Captain returns to his bridge and orders Petty Office Bamford to bring the ship to shore.
At the Greater Maryland Water Reclamation Plant, Follmer does not see Doggett, getting pulled further into the water tank by a naked Shannon McMahon. When Follmer is out of view, McMahon places her mouth over Doggett’s to blow air into his lungs. The next morning, Reyes and Skinner are summoned to Follmer’s office. They are being reined in on the X-file case they are pursuing. Follmer warns Reyes to distance herself from Doggett to save her career, but she accuses Follmer of having his own agenda against her partner. Doggett, meanwhile, wakes up in his bed, alive. McMahon is in his apartment. She tells him that she and Knowle Rohrer were both transformed into “Super Soldiers” who can’t be killed. Although they were the original experiments, the program has since expanded to produce many more of their kind. She, however, hates what she has become, and she asks Doggett for help in exposing the men who are altering the water supply.
Skinner asks Scully why she is getting herself mixed up in Doggett’s investigation when she was the one who specifically requested that Skinner let it lie. She admits that something unexplainable happened with her baby. She is afraid to tell Mulder, because he will want to come back, and that will place him in danger. Doggett and Reyes call Scully to Doggett’s apartment. McMahon explains to her that a chemical called chloramine has been added to public water supplies. Although the substance is usually harmless, the molecular structure of this chloramine has been altered to promote the mutation of offspring. This mutation will breed a generation of Super Soldiers. Scully is at first hesitant to accept the woman’s claims, but then she sees the familiar reptilian ridge at the top of McMahon’s spine. However, a medical examination shows that McMahon is, by all accounts, a normal human being.
After waiting at the Baltimore port with no word from his superiors, the Captain unsuccessfully tries to contact Carl Wormus at the Environmental Protection Agency. He then finds that Officer Bamford has been replaced -- by the presumed deceased Knowle Rohrer. Bamford’s body is found floating nearby. Meanwhile, Follmer suspends Doggett from the FBI, and Doggett lashes out at both Follmer and Deputy Director Kersh over a turf war for the X-files. The Lone Gunmen show Reyes that they have tapped into the EPA’s phone system and found calls to Carl Wormus. The calls were made after the man drowned. As they flip open their laptop, another call comes in, and Frohike answers as Wormus. It is the Captain, instructing Wormus to notify the FBI about the lab on board his ship. As the Captain asks for Wormus’ help in exposing the inhumanity, Rohrer uses his extrasensory hearing to listen to the conversation from far away.
After finding that McMahon works for the Justice Department, Reyes pleads with Follmer to obtain the woman’s files. She then reports to Doggett and Scully that McMahon is not to be trusted. The two men she killed were actually trying to expose the water contamination program. McMahon is using Doggett to get to the third whistleblower -- the Captain. The three agents go down to the Baltimore docks to meet the Captain, but they find Knowle Rohrer instead. Scully and Reyes run off while Doggett tries to defend himself against the Super Soldier. Rohrer is about to kill Doggett, when McMahon appears and slices off Rohrer’s head. Suddenly, Rohrer’s bloodied hand rips through her torso, and she and Rohrer’s headless body both fall off the pier into the water. Doggett goes onto the ship with Scully and Reyes in search of the Captain. They see the Captain’s decapitated head on the ground, but the ship is otherwise empty. Doggett stumbles upon an already detonated bomb, and he hurriedly gathers up Reyes and Scully in the ship’s lab. Scully is reluctant to leave when she sees that whoever was on the boat was manipulating ova for transplantation. Doggett forcibly pulls her out before the ship explodes.
Two days later, Kersh reads Doggett’s report on the case. Although he accounts for Super Soldiers, a naval ship and a conspiracy in the government, he does not mention Kersh in the investigation. Doggett admits that he could not find any wrongdoing on the Deputy Director’s part, but he knows that his hands are indeed dirty. Kersh tells Doggett that he warned Mulder to leave to protect his life. Knowing that Mulder wouldn’t leave only on Kersh’s recommendation, Doggett realizes that Scully was the one who pushed Mulder to go.
Under the dark water, Shannon McMahon’s body lies at the bottom the ocean. Although she appears to be lifeless, her eyes pop open.
Scully is woken by William’s cries, and she soothes him back to sleep. When she turns out the light to go back to bed, the mobile over his crib slowly turns on its own.