“Colony” is episode sixteen of season two of The X-Files.
Mulder starts the episode talking about his sister’s disappearance and how he sustained his faith in extra-terrestrial live even though it resulted in sacrifices to his career, his reputation and himself. A U.S. Navy helicopter is landing and Mulder is taken from it on a stretcher and put into a military ambulance. He’s taken to hospital and Scully manages to get in, even though soldiers tell her she can’t. Mulder is in a bath of water; his narration says that there is intelligent life here among us, and they’ve begun to colonise. Mulder’s doctor says that he is suffering from extreme hypothermia. Scully tells them to get him out of the water; the cold is the only thing keeping him alive. then Mulder flatlines.
Two weeks earlier in the Beaufort Sea, a crewman on the research vessel Alta tells the captain he has to see something. A UFO has been buzzing them. There’s a hovering light in the sky which then does a flyby. It then crashes.
At a clinic in Pennsylvania, there is an article on the news about this and how it turned out to be a Russian plane, with the fighter pilot recovered. A doctor is watching this. There is footage of a man being pulled out of the water, a man who has since disappeared. The doctor flees and is grabbed in the stairwell by the so-called Russian pilot. The man wants to know where someone is. The doctor doesn’t know. The man stabs the doctor in the back of the neck and green liquid starts frothing out. The man starts a fire, then leaves.
Mulder tells Scully when she arrives that someone sent him an email containing three obituaries. He doesn’t know who sent it. Three doctors, who all work in abortion clinics, have died in separate arson fires. It sounds like militant right to lifers. It Mulder a while to figure out why he got the email; then shows Scully photographs of all three victims. Who are identical. There is no blood connection between them; in fact, there are no records at all of the men.
They are told by a Sergeant Dixon that a Reverend Sistrunk has threatened abortion doctors before. He’s been brought in and had a newspaper clipping, showing the dead doctor with the headline ‘Do you know this man?’ They are going to issue an inditement and Mulder mentions the remains not being found. This has not been made public; Mulder explains there are two similar cases with no body. Sistrunk is brought in. He says that some endorse killing in God’s name; he is not one of them. He tells them where he got the newspaper clipping from.
At the paper, the reverend didn’t place the ad. The man who did didn’t leave a name or address and paid cash. He asked for a second week but never came to pay. Scully doesn’t like the sound of this and is concerned it’s a setup. Mulder thinks a setup would have given them more to go on. He checks the map, locating where the victims were killed, and asks the woman at the paper about the number. It’s a voicemail and to access it they can pay the bill. There are a bunch of messages, one about another doctor in Syracuse.
An agent, Weiss, at the field office is contacted. He heads to the man’s home and is going to knock when he hears something. The doctor is told by the man from the crash that his plan isn’t going to succeed. Then he’s killed the same way. Weiss confronts the killer, only to see the doctor’s body turn to green foam. That’s why no body was discovered. Shooting the killer causes him to bleed more green stuff. The last time this sort of blood was seen it had a bad effect, and it does again. When Mulder and Scully arrive, Weiss tells them that he didn’t find the doctor. Well, that’s odd. Then he returns to his car and opens the boot. A dead Weiss is inside it. Fake Weiss shifts into the killer and leaves. Back at the FBI, Skinner calls Mulder into his office. People are not happy. Weiss was found dead.
Scully has received an email about another doctor, this one in Washington. As Mulder arrives at that place he is greeted by a man, CIA Agent Ambrose Chapel. He has a story to tell. Chapel explains that they’ve known about the existence of the men for a decade. They are clones, created by the Soviet Union, sent into the country to damage medical items during a war. They are called Gregors. The killer is cleaning up in exchange for giving details on the programme. Chapel says he placed the ad.
The local doctor leaves a facility in a warehouse in Germantown, Maryland, and returns to an apartment, taken by a woman. Mulder, Scully and Chapel arrive; when the doctor sees Chapel when they come to his door, he leaves by jumping out of the window. They were several stories up. This doesn’t prevent him from getting up and running away. Chapel is the killer.
Mulder trusts Chapel but Scully does not. He also gets a heck of a surprise during the episode.
The story continues in the next episode, “End Game”.