Carl Wormus, an EPA official, picks up a beautiful woman, Shannon McMahon (Lucy Lawless), in a Baltimore bar. While he is driving her home, she forces the car off a bridge and holds Wormus underwater until he drowns. Later, Monica Reyes (Annabeth Gish) meets FBI Assistant Director Brad Follmer (Cary Elwes) in his office, where he hands her two videotapes from the night Dana Scully's (Gillian Anderson) son was born. The tapes show no evidence of the paranormal events John Doggett (Robert Patrick) has reported. Doggett goes to Fox Mulder's (David Duchovny) apartment to consult him, but finds it empty. Meanwhile, McMahon surfaces at a water reclamation plant and drowns a worker there.
Scully refuses to disclose Mulder's whereabouts to Doggett, Meanwhile, Assistant Director Walter Skinner urges him to drop his investigation of Deputy Director Alvin Kersh's (James Pickens, Jr.) actions against the X-Files. Doggett tries to contact some of his old friends from the Marine Corps to find out what happened to Knowle Rohrer (Adam Baldwin); one of them turns out to be McMahon. Meanwhile, at FBI headquarters, an unseen figure slips Wormus' obituary to Reyes. Scully's baby causes the mobile of his crib to spin without touching it. Scully is shocked, contacts Doggett, and tells him to continue his investigation. Scully also performs an autopsy on Wormus' body, where she finds fingerprints on his ankle. After leaving, Scully and Reyes see McMahon, who removes the body from the morgue. Follmer, whom Kersh has ordered to rein in Doggett, arrives at the scene and accuses Scully and Reyes of moving the body.
The Lone Gunmen find that Wormus had been receiving data from Roland McFarland, the drowned reclamation worker. Doggett breaks into McFarland's office with Skinner and finds files on chloramine, a mutation-inducing chemical, before Follmer arrives. Doggett slips into a filtration tank to hide, but is pulled deep underwater by McMahon
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