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 Doggettís to blow air into his lungs. The next morning, Reyes and Skinner are summoned to Follmerís 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 ìSuper Soldiersî who canít 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 Doggettís 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 Doggettís 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 womanís claims, but then she sees the familiar reptilian ridge at the top of McMahonís 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. Bamfordís 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 EPAís 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 Wormusí 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 womanís 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 Rohrerís head. Suddenly, Rohrerís bloodied hand rips through her torso, and she and Rohrerís 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 Captainís 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 shipís 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 Doggettís 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 Directorís 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 wouldnít leave only on Kershís recommendation, Doggett realizes that Scully was the one who pushed Mulder to go.
Under the dark water, Shannon McMahonís body lies at the bottom the ocean. Although she appears to be lifeless, her eyes pop open.
Scully is woken by Williamís 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.
HAPPENED TODAY II”
Original Air Date: 11/18/01
Written by Chris Carter & Frank Spotnitz
Directed by Tony Wharmby
GILLIAN ANDERSON as Special Agent Dana Scully
ROBERT PATRICK as Special Agent John Doggett
ANNABETH GISH as Special Agent Monica Reyes
MITCH PILEGGI as A.D. Walter Skinner
Cary Elwes as A.D. Brad Follmer
James Pickens, Jr. as Deputy Director Kersh
Lucy Lawless as Shannon McMahon
Adam Baldwin as Knowle Rohrer
Bruce Harwood as Byers
Tom Braidwood as Frohike
Dean Haglund as Langly
Ryan Cutrona as The Captain
Ben Reed as Young Officer
Jeff Austin as Dr. Nordlinger
Victoria Gallegos as Follmerís Secretary
Kevin E. West as Navy Seal
Travis Riker as Baby William
James Riker as Baby William
Wyatt Smith as Baby William