Written by Howard Gordon and Frank Spotnitz
Summary by MaraKara
Internal dating: The episode begins on April 27th 1997. Note that this is after "Demons", two episodes later in the run.
In Desmond Virginia, a woman working at an overnight express office named Jane Brophy sneaks away from her post. Hiding in the ladies room, she smokes a cigarette in a bathroom stall. Bees start coming through the overflow ducts of the wall sinks. Within minutes, thousands of bees are in the ladies room. Eventually Jane sees the bees and the bees find Jane. She is stung to death by a swarm of bees. A co-worker finds her dead body on a toilet. The bees are gone, but their stingers litter the floor.
In Fox Mulder's office, a picture of Jane covered with bee stings is sitting in his e-mail files. Walter Skinner is at his computer -- deleting these files and all files connected with this case. Skinner turns off Mulder's computer and leaves the basement office.
The Credits Roll: The Truth is Out There.
Later that night, Skinner takes his phone off the hook. Dressed a black jacket, a charcoal grey sweater and black slacks, Skinner takes a black duffel bag and leaves his apartment. He travels to the overnight express office's ladies room where he starts to remove evidence. He flushes Jane's cigarette down the toilet. He collects the stingers with a hand vacuum and washes the lavatory floor. After noticing some substance dripping from the ceiling, Skinner wipes it clean. After scrubbing the restroom wall and washing the mirrors, Skinner leaves.
Skinner's next stop is the County Morgue where the bee stung body of Jane Brophy is held. After making enough noise to almost tip off an intern, Skinner steals Jane's body. At an incinerator some miles away, Skinner dumps Jane's body into a furnace. Watching the body burn to ashes, Skinner looks troubled by his actions.
Skinner's final stop for the night is the Desmond Police Department. Skinner, now wearing a black baseball cap, shows a fake ID -- he's passing himself off as Fox Mulder. He asks the desk sergeant to see the forensic evidence taken from Jane. After reluctantly signing Mulder's name for the blood workup, Skinner switches a vial of Jane's blood with a vial of blood he had hidden in his hand. After wiping his prints from the pen and blood vial, Skinner races out of the precinct.
Just as he disposes Jane's blood vial a garbage dumpster in the parking lot, Skinner is confronted by a detective named Ray Thomas. Thomas is the officer who e-mailed the real Mulder the pictures of Jane's dead body and asked for help. Skinner blows Detective Thomas off, saying the case isn't worth his time. Thomas is angry but Skinner just drives off.
Skinner and Thomas were watched by "The Grey Haired Man", CSM's flunky who shot and killed X and tried to kill Mulder in the fertility clinic in "Memento Mori".
Back at his apartment at 4am, Skinner strips and puts his overnight wardrobe into a trash bag. After he hangs up his phone, he goes to his front door to dump the trash bag of clothing. Mulder is just walking up to Skinner's apartment door. He tells Skinner that he's been trying to call him for hours. As usual, Mulder wants some answers.
Mulder tells Skinner that he has photos of the dead girl. Skinner seems surprised that Mulder has the hard copies of the photos. Mulder tells Skinner that he had these photos e-mailed to him, but someone destroyed his e-mail files. Mulder got the photos when he was questioned by Detective Thomas's partner. When Skinner asks why Mulder was questioned by Thomas's partner, Mulder tells him that Thomas is dead -- killed after a confrontation with "Fox Mulder".
Mulder suspects that the guy who killed Detective Thomas is the guy who posed as him and probably dumped his computer files. Alarmed, Skinner wants to know what Mulder wants to him to do. Mulder is just asking for help. Skinner asks why Scully can't help Mulder.
A reluctant Mulder tells Skinner that Scully is in the hospital, back for some imaging results. Her oncologist was unhappy with some micro-organisms in her last blood test. The cancer may be metastasizing. Skinner, sickened by the news, agrees to help Mulder. Skinner meets with CSM and the Grey Haired Man in his garage. Actually, the Grey Haired Man almost runs Skinner over with his car. Passenger CSM leaves the auto and is confronted by Skinner. Skinner is furious that the innocent detective was killed. CSM coolly tells Skinner that the detective was killed because he was a witness to Skinner's work.
Skinner tells CSM that he's done everything he was asked since they struck and wants to know why the detective was killed. CSM disagrees -- the detective had to be killed and Skinner is in no position to be question the terms of the deal. Skinner walks away from his deal with CSM. CSM says walking away from deals is not that easy.
Several hours later while he is dozing on his couch, Skinner is awakened by his phone. A very agitated Mulder is on the other side of the phone. He is in a panic -- Jane's body is gone, the restroom has been wiped clean of evidence and the blood work has been changed. Mulder tells Skinner that Jane had a rare blood disorder. The original blood sample showed that disorder, the current blood vial does not.
Skinner asks if there are any suspects. Mulder says no, but he has an ID on the gun that killed the detective. It is a Sig Sauer P228, a standard FBI and law enforcement issue gun. Skinner is surprised. Walking over to his desk, he learns his gun has been stolen. Mulder tells Skinner he is running a search of all owners of Sig Sauer P228's.
A very upset Skinner calls CSM. Skinner's gun was used to kill Detective Thomas. Skinner threatens to turn State's evidence on CSM but CSM says the only person who did anything in relation to this case that can be proved is Skinner.
Skinner wants to know why Thomas was killed. CSM tells Skinner that Thomas died for Skinner -- died for what Skinner wants, a cure for Scully. Skinner tells CSM that Scully is back in the hospital and if anything can be done for her, it needs to be done now. CSM tells Skinner he is well aware of Scully's condition. Agent Scully, according to CSM, "stands to live a long and healthy life" if Skinner keeps quiet.
At the postal center, Skinner makes an official appearance. As he reinspects the bathroom, he notices the substance dripping from the ceiling are back. It is honey. Breaking into the wall near the ceiling, Skinner finds a bee hive.
Skinner takes a part of the hive to a forensic entomologist who works out of a lab in his Maryland home. Claiming security troubles with the FBI labs, Skinner wants the hive studied in secret. The entomologist finds a bee larva and tells Skinner he can probably have info on what kind of bees made the hive after the larva hatches. As Skinner leaves, the entomologist asks Skinner is this has to do with a case an agent named Mulder brought to his attention several months ago. Skinner says no.
Skinner returns to Mulder's office and looks thorough his files on the Canadian bee farm in the season premiere. Skinner notices some of Mulder's correspondence with Marita. He tries to copy Marita's phone number from Mulder's roledex, but Mulder returns to his office. Skinner tries to pass off his presence as writing Mulder a note looking for an update on the case.
Mulder, a bit surprised to find Skinner in his office, shows the AD surveillance photos from the police parking lot. Mulder has a very grainy shot of Detective Thomas talking to "Fox Mulder". Mulder is working with the police photo lab to get a clear shot of the man in the picture.
Skinner leaves Mulder and calls Marita. She tells him what she told Mulder all those months ago: the Canadian bee farm does not exist. Marita wants to know if Skinner knows anything about it. Claiming he might, Skinner tells her he will be in touch. Marita seems surprised.
The entomologist goes to check on the bee larva. The bees have multiplied a thousand fold. Within minutes, the bees have swarmed on the entomologist and killed him.
The next day, Mulder brings Skinner to the morgue. The entomologist is dead not of bee stings but Small Pox. Skinner tells Mulder that is impossible, Small Pox no longer exists. Mulder disagrees, the Small Pox that killed the entomologist is an especially rare and virulent version of the disease.
Mulder has a theory -- the bees are being used to as a delivery system to bring back Small Pox. Small Pox, Mulder reminds Skinner, killed more people than any other contagion known to man. Mulder also tells Skinner that the FBI tech in the photolab pulled an all nighter -- he should be done with the photo of the parking lot "Fox Mulder" soon.
Skinner learns from the overnight express worker that they work in the damaged goods division. He wants and gets a list of all damaged packages in the Desmond office that day. The package with the bees was a going to a post office box in South Carolina.
Back at the photo lab, the tech has done as much with the photo as he can. When the real Mulder gets a good look at the parking lot "Mulder", the real Mulder is shocked, disappointed and angry.
In New York City, CSM tells the smoked filled room of Consortium elders that the bee situation is under control. The entomologist's body and home have been sanitized. The First Elder, the heavyset man, asks how CSM has this all under control. CSM alludes to his deal with Skinner. The Elder asks if the trial run is ready, CSM tells him it is under way.
In a school playground in Payson, South Carolina, a teacher and her students are enjoying recess. Bees start swarming in the school yard, stinging the children. A stampede of kids race into the school but a young boy named Kevin is knocked to the ground. As his teacher saves him, she becomes the center of the swarm and is killed.
Skinner arrives at Payson Community Hospital. The children are very sick. Skinner implores the doctor handling the bee stings to test the children for Small Pox and vaccinated the other children in the community for the disease. The doctor thinks Skinner is wrong -- Small Pox hasn't been a problem for more than seven years. A group of military doctors enter the emergency room, as does Marita.
Seven packages, according to Marita, were sent to a post office box in Payson from a location in Canada. She wants to know what Skinner knows about these packages and what happened. Skinner agrees with Mulder's theory -- the bees are carrying Small Pox. Marita wants to know what Mulder and Skinner know, but Skinner isn't talking.
Skinner returns to his apartment at 11:02pm. As he picks up his phone to make a call, he notices his desk draw has been broken into. As he opens his file draw, his gun is back. Before he can finish making his call, Mulder emerges from the shadows. Angry, Mulder has his gun on Skinner.
Skinner tries to explain to Mulder that he was about to call Mulder.
Mulder, however is furious. "How does it feel to shoot an innocent man in the head?", asks Mulder.
Skinner: "I didn't kill him."
Mulder: "You're a liar. You've been working with the Smoking Man all along. You knew when he had my father killed and you knew when they took Scully"
Skinner tries to explain to Mulder that he was set up and shows Mulder his broken desk draw to prove it.
Skinner: "If I've lied to you....I have lied to you and I won't make excuses to you for those lies but there is a reason for what I did. One that I think you are in a unique position to understand. I advised you against a certain course of action some time ago concerning Agent Scully. I didn't follow my own advice."
Mulder, still wary of Skinner, takes Skinner's gun in for tests. Ballistics prove that Skinner's gun killed Detective Thomas, but the serial numbers from the gun were filed off. Mulder lies about where he found the gun -- under a sewer cover a block from the crime scene. Skinner is surprised that Mulder covers for him.
Later that night, CSM returns to his apartment to find a very angry Walter Skinner waiting for him in the dark. Skinner pulls a gun on the CSM and tells him that "Agent Scully is dying and you haven't done a damn thing about it."
CSM tries to defuse the situation, "Your's isn't the first gun I've ever had pointed in my face Mr. Skinner. I'm not afraid to die. If you kill me now, you also kill Agent Scully."
Skinner: "You have no intention of saving her, you never did."
CSM: "Are you certain? I saved her life once before when I had her returned to Agent Mulder. I may save her life again, but you'll never know if you pull the trigger. Will you?'
Skinner is torn as CSM's telephone begins to ring. CSM tells Skinner to either shoot or let him answer the telephone.
Skinner fires his gun three times and leaves.
CSM is alive but shaken. Bullet holes fill his wall. When CSM answers the phone, Marita is on the phone. She is waiting for orders -- what will she tell Agent Mulder about the bees. CSM tells her to tell Mulder what he wants to hear.