In the opening scene, a biological science team is doing secret work on board a merchant ship. Follmer warns Reyes to cut the shenanigans, but she thinks he's just trying to get Doggett fired. Meanwhile, he's revived by McMahon, who says she was just keeping him hidden from Follmer's agents; she also says that she's a biologically engineered super-soldier devoid of such weaknesses as the need to sleep and the inability to breathe underwater. She tells Doggett that the two men she killed were "preparing the water supply." The ship makes port in Baltimore, and the captain tries to call the dead EPA administrator; he returns to find that Rohrer has taken over as second-in-command (in a rather deadly fashion, as we see later).
Doggett and Reyes invite Scully over to hear what McMahon has to say: the chloramine additive will lead to the mutation of human offspring into super-soldiers like her. The Lone Gunmen discover how calls are being made to the EPA administrator, and Frohike impersonates him as the captain calls begging to have the horrors on board the ship exposed. Reyes finds that the two men McMahon killed were whistleblowers on this latest conspiracy, meaning she's lying about her motives. The captain takes a hostage to try to get the scientists' data to expose, but ends up getting killed by Rohrer.
Doggett, Scully, and Reyes show up at the ship. Rohrer presents a bit of a problem before McMahon shows up and their struggle takes them underwater. Investigating the ship, Doggett finds a bomb on a timer and Reyes and Scully find the lab. Scully realizes that they're manipulating ova for transplantation and wants to see if she's among them, but is forced to flee with her comrades before the ship explodes. Doggett tells Kersh he hasn't found anything concrete on him, but figures his hands are dirty. He turns in his badge and his gun, but takes them back after Kersh hints that he's actually on his side (and was the one who leaked the administrator's obituary to Doggett); Follmer is less certain, thinking Kersh has Doggett just where he wants him.
The episode is dedicated to the memory of Chad Keller, a friend of Chris Carter's who was killed on Flight 77 during the September 11, 2001 terrorist attacks about two months before the episode aired.
Episode Body Count
Petty Officer Bramford: apparently killed by Rohrer, his body is found near the Valor Victor.
Captain: beheaded by Rohrer.
Both McMahon and Rohrer presumably survive their fight.
Cumulative Body Count (184/202 episodes, 1/2 movies)
Humans: 2,107Creatures: 129
Grand Total: 2,300