Curt Delario comforts Nora Pearce as she mourns her husband. "How does a 41 year-old man just wither away and die?" she asks. Since no one can provide her an explanation for Ray's death, she is convinced that he suffered from Gulf War Syndrome, and she wants someone to pay. Leaving her house, Curt turns his car out of the driveway but skids when he sees something in his path. He plows right into a man, but instead of crushing him, the car splits around the man. Curt looks through the shattered glass to see his friend, Ray Pearce, standing in the middle of the hood, unharmed. Ray shoves his fist through the windshield to grab Curt, who screams out in terror.

The next morning, Doggett and Scully scan the crime scene. The car is torn in half and Curt Delario is missing. They find him in a trash can with five deep puncture marks in his head. The autopsy reveals that he was not killed by the impact, but rather by the wounds inflicted when he was pulled through the windshield. Blood and fingerprints on the car are from the recently deceased Ray Pierce. Ray wakes up at St. Clare's Halfway House, unharmed. He pulls shards of metal out of his face.

Doggett goes to the Pearce house. Harry Odell, the owner of the Southside Salvage yard where Ray and Curt both worked, is there. Doggett asks Nora about Ray's cremation because no record of the event exists. He wonders if Ray might still be alive and is somehow involved in Curt's death. Nora rebukes this, insisting that Ray was so sick before he died that he couldn't even walk or lift his head. At the salvage yard, Harry is hurriedly feeding Ray Pearce's employee records into a shredder when Ray himself enters the trailer office. Harry grabs a gun from his desk and shoots. Ray is blown clear out of the trailer. Outside, Harry sees Ray's severed hand, which twitches. Small, interlocking metal pieces begin to repair the limb. Ray comes up behind him, unfazed by his bloody gut and missing arm. He grabs Harry's head and punctures the man's skull with his fingers.

In checking out the aftermath, Doggett notices blue paint on Harry's fingernails. He pulls a half-torn paper out of the shredder -- an invoice from Chambers Technologies. The person on the invoice, Dr. David Clifton, no longer works there. His successor, Dr. Puvogel, tells Doggett that Clifton was working on a smart metal that can regenerate itself. He also says that their company would have no use of any local salvage yards. Scully phones Doggett from the morgue, informing him that Ray's cell makeup was affected by exposure to a non-identifiable metal. Tests show that his blood has enough metal alloy to kill an elephant. At the halfway house, volunteer social worker Larina sees a news report on Harry Odell's murder, recognizes Ray and phones Ray's wife.

Ray pursues Dr. Puvogel, and the agents lure him to Chambers Technologies. Ray gets captured in a test chamber and his fists dent the four-inch metal doors. He escapes by ripping open the thick metal of the back wall. Blood left on the jagged wall begins to turn itself into metal. Remanding Dr. Puvogel to safety, Doggett notices that a row of stacked barrels are painted the same color blue found on Harry Odell's fingers.

Nora waits for her husband at the halfway house, and asks him why he didn't contact her. "I'm not me," he responds, before showing her that his body is a mix of flesh and metal. He tells her that the people who did this to him must pay. At Southside Salvage, Doggett uncovers blue barrels with the Chambers Technology logo underneath the paint. When he turns one over, a think river of silver liquid pours out with a human body made of metal. It is the missing Dr. Clifton. Scully and Doggett question Puvogel, who tells them that Clifton got poisoned from working on an alloy with genetic material in it. Puvogel was aware that Clifton was dying, but did not know how his body was sent to the salvage yard. Suddenly, Doggett sees Nora Pearce sneaking around the Chambers hallway. She is searching for the name of the person responsible for her husband's disfigurement, but is caught before she gave the name to Ray. A SWAT team is sent to the halfway house, but they are too late. Ray kills Larina and escapes. Scully and Doggett beg Nora for her help in preventing Ray from hurting anyone else, and she agrees to have her house watched by the police. Ray slips in and persuades Nora to tell him the name of the person from Chambers Technologies who made him inhuman. When he leaves, Nora rushes out of the house, hysterical. She tells the police that her husband had just been there and that he is going to kill a man named Owen Harris.

Ray intercepts Harris' car, pulls him from the driver's seat and says "You made me." The man's wife and child scream in terror. Harris doesn't understand because he's only an accountant and had waste transferred to Southside Salvage because he was told to do so. As Harris' son cries in the backseat, Ray's eyes blink with the last light of kindness left in him. He lets the man go.

Later, Doggett and Scully arrive at the scene. Harris is alive, being treated by a medic. The agents are puzzled as to why Ray didn't kill him, but Scully surmises that Ray's body had died, and what was left was a machine. Whatever bit of humanity was still in him may have saved Harris.

At Southside Salvage, a car gets dumped into a compactor. Ray is inside the crushed car, calmly accepting his inevitable conclusion.