Jane Brody, a mail sorter at an overnight delivery company, sneaks into the female employee's rest room to smoke a cigarette. Without warning, hundreds of bees creep into the stall where Jane is sitting. When the young woman attempts to swat the insects so she can escape, the bees swarm and attack, stinging her to death.

An e-mail file containing photographs of the victim is sent to Mulder, but Skinner intercepts and deletes the file. Skinner then covertly erases evidence of the bee attack, and incinerates Jane Brody's body. Identifying himself as Fox Mulder, Skinner visits a police forensics lab in Virginia where he switches a vial containing Brody's blood with another identical container. As he is leaving, Skinner is approached by Detective Ray Thomas, the man who e-mailed Mulder photographs of Brody's body. Skinner tells the disappointed Thomas (who thinks he is talking to Fox Mulder) that the evidence does not warrant his further involvement in the case.

Mulder pays Skinner an unexpected visit. He states that someone has gone to great lengths to keep news of the bee attack from reaching him. He also reveals that Detective Thomas was found dead, the victim of an execution-style shooting. With Scully undergoing tests at a hospital for the treatment of her cancer, Mulder asks Skinner for his help in solving the mystery. Later that night, Skinner is approached by The Cigarette-Smoking Man. Skinner accuses him of murdering Detective Thomas. The Cigarette-Smoking Man counters that Skinner "failed to neutralize a potentially compromising situation."

Mulder discovers that someone stole Brody's body from a morgue and switched her blood sample at the police station. He also discovers that Thomas was murdered by someone using a government issue gun. Shortly thereafter, Skinner realizes his own weapon is missing. Skinner revisits the women's rest room where Brody was killed. He discovers part of a massive honeycomb inside the rest room wall, and brings a piece of the honeycomb to entomologist Peter Valdespino for analysis.

Mulder discovers that a bank surveillance camera captured a blurry image of someone talking to Detective Thomas shortly before he was murdered. He hopes the Bureau's Photo Unit can produce a clearer image of the man who he suspects is Thomas' killer. Using larvae taken from the honeycomb, Valdespino hatches more bees to identify the species. The insects unexpectedly swarm the entomologist, killing him. Mulder later discovers that Valdespino died from smallpox. He hypothesizes that someone has engineered a method of spreading the contagion using the insects.

Skinner questions Brody's co-worker, Misty Nagata. She reveals that a damaged overnight package was confiscated by other investigators working on the case. Students at an elementary school in South Carolina are attacked by a swarm of bees. Skinner tells doctors at a hospital emergency room that the children should be treated not for bee stings, but for smallpox.

Working from surveillance camera footage, the FBI photo unit produces a clear image of Skinner talking to Thomas shortly before his death. Outraged, Mulder accuses Skinner of working in conjunction with The Cigarette-Smoking Man from the very beginning. But Skinner insists he was framed.

Skinner again confronts The Cigarette-Smoking Man, firing several shots in anger. Afterward, The Cigarette-Smoking Man instructs Marita Covarrubias, in the company of Syndicate members, to tell Mulder whatever he wants to hear.