Assistant Director Skinner is at a gym, in a boxing ring with a sparring partner. He becomes disoriented and gets knocked out, waking up in a hospital. While waiting for a doctor, Skinner's cell phone rings and a scrambled voice says, "it's in you -- you have 24 hours -- you are already dead." The doctor, however, releases Skinner, after drawing blood for some tests, because there appears to be nothing wrong except for a bruise on his ribs.
Later that evening at FBI headquarters, Mulder and Skinner talk. Skinner is on a couch in his office and is having trouble seeing and Mulder calls Scully into the office to consult. They wonder if Skinner might have been poisoned. Retracing his day, Skinner remembers a man who bumped into him in the hallway. They identify him as Kenneth Orgell, a physicist who is an advisor to a US Senate committee. Mulder and Skinner go to see Orgell, who denies that he was at the FBI building, but there are several men in black in Orgell's home. After a chase, Mulder catches one. He has Tunesian diplomatic papers, so Skinner orders Mulder to release him. Orgell has disappeared with the other men in black. In his house, Mulder finds papers showing Orgell with Senator Matheson, who has occasionally helped Mulder with tips.
Scully goes to talk with the doctor who saw Skinner, Dr. Platte. The blood tests have not yet been done. They find tiny bits of carbon in Skinner's blood. It is unclear what they are, but they are multiplying. Scully eventually finds that the carbon is creating a matrix and building structures in Skinner's blood. Mulder visits Senator Matheson. Orgell has been working on a bill to provide aid to third world countries via expanded exports, but the Senator declines to help Mulder further with the case. On embassy row, Skinner pulls into a parking garage and his car is fired on by the Tunesian. He and Skinner stalk each other through the garage, but as the Tunesian is about to shoot Skinner, a car races through the garage and runs down the Tunesian, killing him. Skinner collapses.
Scully learns that Skinner is being brought back to the hospital. An emergency room doctor is preparing to remove Skinner's arm. Much of his body is now discolored and mottled. Scully barges in and stops the procedure, because the problem is in his blood. In Skinner's office, Mulder finds that Skinner has been doing a security review on export laws involving new technology. He has a phone call from the synthesized voice, and finds that a man is in the hallway using a synthesizer designed for people who are speech impaired. Mulder chases the man, who we see to have long hair, escapes. Soon after, the long-haired man also calls the Senator.
At the FBI impound lot, the car driven by the long-haired man has been recovered. It has strands of wig hair in it, and PCB traces on the tires. The PCBs could come from any abandoned power plant. Senator Matheson arrives at an abandoned power plant and finds Orgell tied up and with the same skin mottling that Skinner has. Orgell swears that he told the FBI nothing. The long-haired man is watching. Meanwhile, Scully has an idea to filter Skinner's blood to try to remove the carbon. Skinner tells Scully he is sorry for not helping her and Mulder more; he always played it safe and didn't take sides. All of a sudden, Skinner remembers seeing a man at the gym and at the FBI office -- with long hair.
Mulder arrives at the power plant and finds the Senator's car. Inside, Matheson tells him that Orgell is dead, killed by the conspiracy. What they put in Skinner is nanotechnology -- tiny robots. They wanted S.R. 819 in order to be able to export the nanites and the Senator claims he is not involved. At the hospital, Skinner's heart stops. As a sheet is pulled over Skinner's body, a hand is seen to adjust a remote control, and Skinner revives. It is the long-haired man.
Three weeks later, Skinner's is doing well. Whatever is inside him is dormant and he is back at work. S.R. 819 has been withdrawn. Mulder thinks it is about the X-Files, but Skinner will not authorize further investigation, which Scully finds odd because of Skinner's comments about helping them more. Later, Skinner enters his car in the FBI parking garage. Alex Krycek is waiting for him and it is obvious that it was he wearing the long hair wig. He tells Skinner that he could press the button and kill Skinner at any time. "What's this all about?" asks Skinner. "All in good time," replies Krycek.