At a fast food restaurant a man pulls out a gun, taking everyone inside hostage. An older man tries unsuccessfully to get him to calm down, but he shoots three people before being shot himself by snipers outside. The older man tells the shooter he's not going to die, and with the palm of his hands heals his wounds.
Agents Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) arrive on the scene to investigate, but find that the healer, named Jeremiah Smith vanished while talking to an investigator on the scene. Meanwhile the Cigarette Smoking Man meets with Mulder's mother at her former summer home in Rhode Island. The Cigarette Smoking Man tells her he called her to ask her to remember something, causing the two to argue while someone photographs them from a distance. Mulder is notified by Assistant Director Skinner that his mother has suffered a stroke and heads to the hospital, where she writes down the word 'PALM'. Mulder and Scully later watch a video of Smith and the Detective, finding that someone else suddenly appears in Smith's place after the Detective looks away.
Smith meanwhile is taken captive by the Cigarette Smoking Man at his place of work, the Social Security Administration and is locked up in a high security prison. Mulder heads to the house in Rhode Island where he meets X, who shows him photos of his mother arguing with the Cigarette Smoking Man. X believes that they argued over something very old and very important. Meanwhile Jeremiah Smith appears at FBI headquarters and turns himself in, saying he has no memory of healing anyone or leaving the crime scene.
Mulder searches through the house and after rewording 'PALM' to 'LAMP' finds an alien stiletto weapon (previously seen in the episodes "Colony" and "End Game") in one of the lamps.
At the prison, the Cigarette Smoking Man interrogates Jeremiah Smith, who has lost faith in the project. When the Cigarette Smoking Man tells him people no longer believe in miracles, but authority and science, Smith morphs into Deep Throat.
Mulder goes to see Skinner, demanding the Cigarette Smoking Man's whereabouts, blaming him for what happened to his mother.
After hearing that Smith came in and gave a statement, Mulder heads to the Social Security Administration to take him in for questioning. Smith flees into a crowd, morphing into someone else.
The Cigarette Smoking Man once again meets with Smith, who this time morphs into Bill Mulder, then reveals that the Cigarette Smoking Man is dying of lung cancer. The Jeremiah Smith that fled from Mulder and Scully heads to the prison and is revealed to be the Alien Bounty Hunter. He heads to Smith's cell in order to kill him, but finds it empty.
Mulder once again goes to see his mother at the hospital and runs into the Cigarette Smoking Man there who tells him that she contacted him about the whereabouts of his sister.
Scully meanwhile looks into Jeremiah Smith and finds MANY OTHER Jeremiah Smiths with the same appearance working at Social Security Administration offices across the country.