Written by Chris Carter and David Duchovny
Directed by Nick Marck

In which Mulder is tipped on a case involving the killing of identical doctors, leading to the discovery of a shape-changing hunter...and the apparent return of his sister Samantha...

Synopsis - Analysis - Memorable Quotes - Observations




As the episode begins, Mulder speaks about how his belief in the circumstances of his sister’s abduction led him on his perilous quest for the truth, as a helicopter descends onto the landing pad of a military hospital. Mulder himself is pulled out of the helicopter on a stretcher, taken directly to a frostbite unit. He is apparently freezing to death. Scully demands to see him, as the doctors place Mulder in a warm bath to raise his body temperature. Mulder, still in voiceover, explains that if he should die now, it would be worth it, because he now knows for certain that alien life exists…and it has begun to colonize Earth.

Scully forces her way to the doctors, demanding that they stop raising his body temperature. Despite all evidence to the contrary, Scully insists that the cold is the only thing keeping him alive. Sure enough, as Mulder’s body temperature rises, his vitals plunge and his heart stops.

Two weeks earlier:

A research vessel in the Beaufort Sea in the Arctic observes a UFO hovering for quite some time over the ship. Without warning, the UFO veers from its position, crashing into an iceberg in the distance. The captain of the ship orders the crew to make for the crash site, so they can recover survivors.

Two days later, at a family services clinic in Scranton, PA, Dr. Landon Prince walks into the break room just in time to hear a news report about the recovery of a supposed Russian fighter pilot in the Arctic. As the reporter describes that the recovered pilot somehow walked out of a hospital in Alaska without being identified, Prince recognizes the pilot with intense dread. He rushes out of the break room, and as he comes through some swinging doors, the pilot is already waiting for him.

The pilot demands to know where “he” is. When Prince doesn’t answer, the pilot pulls out a small metal tube, out of which a long sharp pick extends with a hiss. The pilot drives the pick into the back of the doctor’s neck, and a foaming green liquid begins to pour out. Dropping the doctor, the pilot rips apart a nearby electric box, starting a fire. He walks out as the room begins to burn, leaving the remains of the doctor behind.

Several days later, Scully arrives at the basement office. Mulder shows her three obituaries sent to him through anonymous E-mail. The obituaries are for Landon Prince of Scranton, Dale Gayhart of NYC, and Harvey Buchanon of Teaneck, NJ…all doctors who had worked at abortion clinics, killed in arson fires. After some digging, Mulder was able to figure out why someone thought he would be interested: all three men were identical in appearance, without any documented blood relation.

The agents arrive in Scranton, and meet with the federal Marshall detaining one of the initial suspects, a preacher known for threatening abortion doctors. He was found in the area, carrying a newspaper clipping of an ad showing the face of Prince and the other victims, and a phone number to call if someone with that appearance had been seen. The Marshall explains that no remains have been found, something in common with the other two murders. A quick interview with the preacher reveals that while he appears to have the will, he is not the one committing the murders. The preacher tells them that he found the ad in a paper in Binghamton, NY.

Mulder and Scully ask about the ad at the office for the paper. A woman behind the front desk tells them that a man placed the ad for a week, and then called to extend it without paying. The preacher, however, was not the one who placed the ad. Scully is concerned about the complete lack of information, as well as the questionable source of the information. Mulder, however, notes that the murders have been taking place in a generally northern direction. He asks to hear the voicemail messages for the ad, and the first response on the voicemail is a sighting in Syracuse. Mulder observes that Syracuse is north of Scranton, PA.

Mulder contacts Agent Weiss in the Syracuse, NY field office. He asks Weiss to find and protect a doctor named Aaron Baker until he and Scully can arrive. Weiss arrives at Baker’s house, and when he walks up to the door, he hears arguing inside. As Weiss walks around to the back door, the supposed pilot stabs Baker in the back of the neck. Weiss sees Baker fall to the floor, dead, and he breaks through the back door, ordering the pilot to drop his weapon. But when Weiss looks over at Baker, the body has begun to dissolve in a puddle of foaming green liquid.

The pilot moves to attack, so Weiss fires three shots into the pilot’s body. Instead of blood, however, green liquid oozes out of the wounds. Within seconds, Weiss cries out as he reacts to the liquid, raking at his eyes and choking. But when Mulder and Scully arrive at the house, they are met by Weiss, who claims that everything is fine, and that Baker is out of town. As the agents go to look for themselves, Weiss opens the trunk of his car. The real Weiss is inside, stripped, bound, and gagged, terribly inflamed wounds around his eyes, nose, and mouth. The other Weiss shifts his appearance to that of the pilot, who tosses the keys into the trunk, slams it shut, and walks away.

A couple of hours later, Mulder is called into Skinner’s office. Skinner wants to know what Mulder thought he was working on, especially since nothing was authorized. With Weiss found dead, Mulder and Skinner are on the hot seat. Mulder is stunned, but Skinner doesn’t want excuses. He effectively forbids the agents from pursuing the case further.

Scully calls Mulder in the office, and is equally stunned by the turn of events. However, she has unsettling news of her own. They both received another E-mail, giving the location of another doctor named James Dickens…this time, in DC. Mulder decides to ignore Skinner’s warnings and go pick Scully up to investigate. But when he arrives, a CIA agent named Chapel approaches him, claiming to have information on the case.

Chapel tells the agents that in the early years of the Cold War, the Russians developed a method of creating clones. According to Chapel, these clones (named “Gregor”) were smuggled into the United States and placed into strategic sectors of the medical community. In the event of war, the Gregors would cripple medical supply lines and taint blood supplies. Chapel explains that through a secret deal, a Russian agent was brought in to assassinate the Gregors in exchange for suppressing all knowledge of the project.

Chapel believes that Mulder was contacted by the Gregors because of his reputation for seeking the truth about government activities. Chapel was the one who placed the ad, it seems, in the hopes of aiding that effort. Mulder informs Chapel that they have located one of the surviving Gregors.

Meanwhile, Dr. Dickens leaves a warehouse laboratory in Germantown, MD, where four large vats filled with green liquid are attached to various instruments. He is driven from the warehouse to his apartment by a young woman. When the agents knock on his apartment door, the young woman hides in another room. Dickens is calm until Chapel steps into view. Dickens panics, jumping out of his window, crashing to the ground far below.

However, Dickens recovers quickly, running off into the night. Mulder runs after him, while Chapel sneaks in another direction. As Dickens races across a street, Mulder follows, and gets slammed by a car. Scully sees him hit the ground, but he waves her off, telling her to find Dickens. Chapel finds Dickens in an alley, and Dickens tries to grab a ladder for a fire escape. Chapel shifts into the pilot, and pulls Dickens back to the ground. By the time Scully finds the alley, Chapel is walking away, claiming that Dickens fled to the roof. Scully warily checks the area, and steps in a puddle of sublimating green goo.

The next morning, Mulder is still intact, though clearly banged up. Scully admonishes Mulder for trusting Chapel, especially since she realizes that Dickens was running from Chapel, not them. Mulder thinks that Chapel killed Weiss as well. Mulder offers that she should be the one to explain that to Skinner, and Scully counters that Mulder is too willing to risk everything and everyone to pursue a case. Mulder, however, feels that it’s part of the risk for working with him.

Ultimately, however, Scully continues to discuss the case with Mulder. She shows him one of her shoes from the night before, which has been eaten through by the green liquid she stepped in. Mulder suggests sending the shoe for analysis, while they inspect Weiss’ body. Apparently, no cause of death could be determined. Scully is unable to find any obvious cause of death, but blood work reveals a massive excess of red blood cells. Mulder reminds Scully that Chapel mentioned something about tainting the blood supplies. However, before the agents can continue working, Mulder is called in to speak with Skinner.

Mulder assumes that Skinner is calling him regarding his report, but Skinner informs Mulder that his father has been trying to call. There’s been an emergency in the family. Mulder calls his father’s house, but surprisingly, his mother answers. Mulder asks to speak to his father. Mulder’s father asks him to come home, but doesn’t explain why. Mulder asks Scully to follow up on the investigation in the meantime.

Scully finds an address associated with Dickens, and goes to the location. It’s the warehouse with the giant tanks of green liquid. She arrives just in time to see the pilot, in Chapel’s form, pushing over the vats and destroying the contents. Scully tries to leave before she’s seen, but the pilot watches her drive away. He follows her home and watches her from his car. Scully notices, and leaves Mulder a message, saying she’s in danger.

Mulder arrives at his father’s house in West Tisbury at Martha’s Vineyard. His father Bill is outside, and he greets Mulder in a standoffish way. It’s clear that there are issues between them. As Bill tries to explain what’s happening, Mulder sees a young woman (the one previously with Dickens) sitting with his mother. He’s shocked when Bill tells him that it’s his sister…Samantha.

Mulder runs into the house, hardly able to comprehend what he’s seeing. After helping his mother get to sleep, soothing her fears, Mulder speaks with Samantha. He asks her what she remembers about her time away. She explains that after a time, she was returned to another family. She knew they weren’t her real family, but she didn’t remember anyone else. Then she went through post-hypnotic regression, and she remembered the abductions and tests. Samantha reveals that her adoptive father and other doctors are being hunted by a kind of bounty hunter, and that Mulder was contacted to help save the survivors. Even more shocking, Samantha tells Mulder that the identical men are all aliens, and that the bounty hunter will be coming for her soon.

Mulder takes Samantha to his apartment, and tries to contact Scully. Samantha explains that the bounty hunter can make himself look like anyone. However, for some reason, Samantha can recognize it. Meanwhile, Scully takes a bus to throw off Chapel’s pursuit, intending to check out the warehouse before moving on to the Vacation Village Motor Lodge, where she’ll be hiding.

When Scully gets to the warehouse, she picks through the remains of the laboratory equipment. She finds one of the transparent sacs that had been suspended in the green liquid, and inside is a dying fetal-type creature. It looks vaguely alien. Before she can continue, she hears a noise, and sees someone running out of the room. She chases him down, and when he turns around, she sees that it’s one of the surviving Gregor clones. Soon, there are four of them, asking her for protection.

While Scully helps place all four men in protective custody, the bounty hunter watches from the roof. Mulder, meanwhile, tries to call the Vacation Village Motor Lodge, but Scully doesn’t arrive until after Mulder calls. The bounty hunter sneaks into the federal stockade where the Gregors are being protected, using the guise of an FBI agent to get past the guards. All of the Gregors recognize the bounty hunter, and know they are about to die.

Later that night, Scully is awakened by a knock at the door. It’s Mulder, and he says that he got her message. Before he can say more, her cell phone rings. It’s Mulder…and immediately Scully stares at the man standing in her room with terror…


As of “Colony” and “Endgame”, the mythology of the series began to display an odd bit of split personality. The government conspiracies and spiritual questions surrounding the X-Files as championed by Morgan and Wong would continue to be explored, but at the same time, the apparent struggle between alien races to control the future of humanity was thread into the story by Carter and Spotnitz, with the aid of Duchovny.

The series would never manage to reconcile those two sides of the mythology with any grace. While the existence of the alien colonization plans was supported by several episodes, the allure of a purely human conspiracy remained. Oddly, that dichotomy was completely unnecessary; the two elements can be easily merged.

This issue is perfect to discuss in relation to “Colony” because this episode, along with “Endgame”, is nearly impossible to understand in the context of the mythology as it was eventually explained. The bounty hunter in this episode would be revealed as one of a series of cloned aliens, apparently some of which work with the Black Oil Colonists, while the rest are leading a rebellion against colonization.

The black oil would eventually be revealed as a sentient alien virus, with the goal of spreading itself (as the most perfect form of life) throughout the universe. At the same time, the Purity virus (through its Colonist hosts) forge a deal to allow the collaborating humans of the Syndicate to use alien DNA to develop a means of hybridizing humans with what is apparently Colonist genetics.

What seems odd, then, is that the bounty hunter in this episode appears to be destroying the efforts by other alien clones to perfect or evolve the hybridization process by using human fetal tissue in genetic experimentation. After all, if the Gregors aren’t working on the Colonist-sponsored experiments, who are they working for, and how would they have come into being? If the Gregors are working within the Colonist-sponsored experiments, and the bounty hunter could be part of either the same effort or the rebellion, how do the Gregors know that he’s a threat? And why, then, would Baker describe a situation where the bounty hunter’s allies are working on something in parallel with their own efforts, as if there were two groups of oddly identical aliens working to different goals?

Other questions come to mind. It’s clear that the green fluid within the test subjects from “The Erlenmeyer Flask” has a similar but lessened effect as the green blood seen in both the Gregor clones and the bounty hunter. Therefore, there is a connection. If the hybridization utilizes the clone DNA, and Purity is concerned with the possible sullying of its genetic perfection, then eliminating forbidden genetic manipulations connects the clone DNA to Purity.

The mythology as it was explained does not cover any of those concerns. If anything, it glosses over those concerns with apparently straightforward phrases that very quickly move on to the next topic, to avoid unpleasant questions! If there’s any doubt that this is the case, “The Truth” proves it out; the primer of the mythology given in that episode barely touches on how all of this clone business was supposed to make sense!

In the course of watching the series, another version of the mythology comes to mind, one that covers all of the bases, while actually allowing the characters themselves to come to exactly the same conclusions as depicted. In essence, the questions are as follows: who knows what about the reality of the struggle, when are characters expressing truths based on lies they believe, and when are characters intentionally lying to manipulate events as they believe must occur?

The mythology, beginning in 1947 and ending in 2012, has four distinct phases. The following is an exploration of those phases as they relate to “Colony”:

The first phase takes place between 1947 and 1973, when the crash at Roswell and discovery of apparent alien incursions around the world sparked at least two efforts (Western and Communist) to create “super-soldiers”. Medical alterations, cloning, radiation treatments, and reproductive experiments were all used to create something that could handle the threat posed by the alien Colonists.

The second phase takes place between 1973 and 1990. At this point, the Colonists altered the course of the experimentation by forcing the Western Syndicate to pursue certain “hybridization” efforts. At the same time, the super-soldier program continued, utilizing nanotechnology to more and more sophisticated levels (the implants, the soldiers of the later seasons). It is very likely that the early cloning experiments evolved into the modified clones seen in this episode, which means that during this phase, something changed. In essence, the introduction of the “alien” DNA in 1973 allowed the creation of clones with the toxic green blood.

The third phase takes place between 1990 and 2002. This is the time period of the series. At this point, the cloning experiments have been successful. Now the reproductive experiments also involve attempts to create viable embryos that naturally develop the green fluid, based on the “hybridization” experiments. Scully’s daughter Emily was, of course, part of the evolution of those experiments, some of which are seen in “Colony”. By the end of the series, one can assume that those experiments are successful, and are utilized by the super-soldiers in taking control of the government.

The fourth and final phase takes place between 2002 and 2012. With the nanotechnology behind the super-soldiers perfected, and the creation and use of cloned shape-shifters representing the success of organic super-soldier development, the final step would be the final evolution to a completely non-corporeal intelligent state. This would meld the best attributes of nanotech super-soldiers (infinite repair capability) with those of the organic super-soldiers (infinite adaptability), with none of the apparent weaknesses. Hence, the eventual creation and spread of Purity.

The trick, of course, is how a future artificially evolved Purity, created by and of genetically engineered humans, could have then appeared to be alien in nature. The genetic engineering covers the apparently extra-terrestrial part, but if Purity is something from the future, how could it appear as ancient, let alone during the series?

Previous episodes, as well as many later ones, point out that the engines used in the so-called UFOs work by warping space and time. It’s simply a matter of scale. Therefore, instead of having various alien factions that somehow appear human and consider Earth to be their playground, one is faced with warring factions of evolved humans from the near future vying for control over the evolutionary path of the human race.

How this fits into the entire mythology shouldn’t be worked out in relation to “Colony”. However, it does pertain, since it provides a very simple explanation for what happens in this episode and “Endgame”. By the beginning of the series, as seen in the later seasons, super-soldiers are a reality. The fact that they can regenerate from nothing (as in “Existence”) suggests the highest level of nanotechnology. Given the position of the vital nanotech, the back of the neck, the implant technology and control systems (related, of course, to that used on Skinner and Scully) are connected.

The next step would be to duplicate the effects of nanotechnology in a genetically engineered human being. Part of the duplication process would involve a control organ roughly analogous to the control implants of the nanotech; hence, the vital organ common to all of the Gregor clones (and as seen, the bounty hunter as well). The Gregors are obviously early cloned versions of the more perfected organic super-soldiers realized in the bounty hunters. For one, the Gregors can’t change their appearances, suggesting that the clones regulate their vital systems using the genetically engineered retrovirus system, but not to the extent that allows them to reconfigure surface tissue.

The post-2002 factions, as depicted on the series, would apparently be those ensuring the creation of Purity by sponsoring and guiding the programs and experiments necessary for that goal, and the rebellion forces acting to preserve the creation of the organic super-soldiers but prevent the creation of Purity. The implication of the later seasons is that the bounty hunter clones were the final testing group in the creation of the organic super-soldiers, sometime around 2002. It is hinted that those clones were allied with the rebellion; only one of them eventually went traitor and worked for the Syndicate/Purity conspiracy.

Given that theoretical framework, the events of this episode come into sharper focus. The bounty hunter, as a member of the rebellion against the Syndicate/Purity conspiracy, came back to this specific time to prevent certain avenues of experimentation from being conducted. The Gregors, having been inserted into the medical establishment for the sole purpose of gaining genetic material for the conspiracy’s experimentation, were the logical targets. The bounty hunter would be aware that historically, from the rebellion’s future point of view, the Gregors were the ones conducting the “forbidden” experiments.

The nature of the organic super-soldiers would require a quasi-corporeal intelligence, aware on levels beyond normal human consciousness. It would be on that level that the Gregors could identify the bounty hunter for what he was: one of the rebellion, and therefore an enemy. But why, then, would Baker have wanted to know why the bounty hunter was killing them?

The answer, of course, is that previous experimentation had led to the creation of the bounty hunters and organic super-soldiers of the rebellion. It was only after the Gregor experiments began succeeding too well in advancing the evolution towards an even more advanced form, Purity, that it all had to be stopped.

Several other aspects of this episode fit into the pattern of the series more closely within this modified framework. This episode shows that Mulder needs to stay cold to survive; that is common to both forms of the super-soldier “virus”, as well as Purity. The Gregors spread throughout the medical industry in key locations, just as the Jeremiah Smiths spread throughout the Social Security system to aid in the cataloging of the US population.

This episode also contrasts sharply with “One Breath”. Skinner seems to be more tentative in his aid to Mulder, especially when the case becomes tied to an agent’s unexplained death. Clearly the conspiracy is aware of the symptoms of exposure to the retrovirus, and they know that keeping Mulder away from Weiss is a very good idea. Indeed, they had to expect that Mulder or Scully would connect Weiss’ symptoms to those that Mulder himself experienced in “The Erlenmeyer Flask”. The fact that he didn’t make the connection, especially when Scully instantly connects the events of “Red Museum” to Purity Control without nearly so much evidence, seems to be a flaw.

Another interesting aspect is the repeated motif of building lies out of the truth. The bounty hunters story of Russian cloning experiments matches what Mulder was told in “Eve”, making the rest of the “Gregor” story convincing. (That, and the timing of the Gregor introduction to US society matches the rough time when the Gregors would have been used to advance the organic super-soldier experiments.)

Even “Samantha” gets into the act. As seen in “Closure”, the real Samantha was abducted and then returned to live with a family while still a test subject. “Samantha” melds those events into her own story to deceive and manipulate Mulder into essentially protecting the work of the conspiracy! After all, wouldn’t the conspiracy know that Mulder, their tool if disinformation, could be easily manipulated with even the hint that Samantha was alive? And wouldn’t they know the details of Samantha’s testing, as well as the details of her abduction?

In light of “Closure”, the reactions of the Mulders make perfect sense. Bill Mulder remains detached, making a point to say that Ma Mulder was the one who called Fox and wanted him involved. It’s clear that the Mulders never expected to see Samantha again. Bill would have been aware of the circumstances of Samantha’s existence until her final disappearance, and therefore highly skeptical. On the other hand, Teena would have come to the same conclusions, but would always want to believe that Samantha was still alive. Regardless, it’s very clear that Bill knew that Fox was being manipulated; however, being detached for quite some time from the conspiracy, he couldn’t know the full details.

Having “Samantha” enter the picture, especially given the fact that Mulder’s the only one who’s supposed to believe she’s still alive, presents problems in the next episode. And in the end, it all becomes a plot contrivance when everything is later revealed. Bill has reasons for keeping his silence with Fox, but why would Teena, especially in such an emotionally traumatic moment?

Equally, in order to get the bounty hunter on Scully’s trail so that the episode can end with the false identity cliffhanger, Scully makes one of the most idiotic decisions possible. Why would she covertly call Mulder about the danger of being followed by a CIA agent, who could have any number of assets in the field, while riding conspicuously in the middle of a packed bus?

It also odd that Mulder, having realized how his crusade could ruin the lives of others in “One Breath”, suddenly develops a complete lack of concern for anyone unwilling to follow in his reckless footsteps. This is especially strange, when it’s Scully that he’s berating for hesitating to take those risks. This episode takes place perhaps two months after “One Breath”, and it’s hard to reconcile Mulder’s attitude.

Most of the problems with this episode, granted, are the result of later mythology revisions that take certain elements of this episode and “Endgame” and use them in completely different ways. Given what had been revealed on the series up to “Colony”, this episode is a stunning series of revelations, with only Scully’s error as a glaring misstep.

Memorable Quotes

MULDER: “You got to wonder about a country where even the President has to worry about drive-by shootings…”

MULDER: “This clipping…where’d you get it?”
PREACHER: “From the newspaper…”

MULDER: “I’d assumed we had an understanding about the X-Files.”
SKINNER: “I’m sure it doesn’t surprise you, Agent Mulder, that the people I have to answer to aren’t quite so understanding.”

SCULLY: “I mean, whatever happened to ‘trust no one’, Mulder?”
MULDER: “Oh, I changed it to ‘trust everyone’. I didn’t tell you?”

SCULLY: “You’ll pursue a case at the expense of everything, to the point of insanity, and expect me to follow you. There has to be somewhere to draw the line.”

MULDER: “Those are the risks we take. You either accept them or you don’t. We all draw our own lines.”


- Ah...one of those infamous David Duchovny voiceovers, where natural language is only a vague memory...

- Why would the bounty hunter have needed to intentionally crash and be rescued? Why not just land, thereby preserving the secret of his arrival?

- How did pulling the cover off the breaker box cause everything to set ablaze?

- Nice “Terminator” homage, though!

- The E-mail that Mulder references in the beginning of the episode sets Dr. Prince’s death as late January, 1995...making the time between “Die Hand Die Verletzt”, “Fresh Bones”, and “Colony” a matter of days...

- Apparently, in the “X-Files” world, it doesn’t snow in upstate New York in January!

- I’m convinced that most of what Baker and the bounty hunter had to say was just random, meant to sound important without actually revealing anything...

- It’s nice to know that Mulder ignores the “seriousness of the matter” in the space of five minutes!

- Note that the date of the E-mail sent to Scully with Dickens’ image is left blank...

- You’d think that Mulder would realize that doctors positioned as abortion doctors would be in the wrong place to contaminate blood supplies and sabotage pharmaceutical companies!

- Why didn’t Scully notice that the green goo was obviously in the shape of a human being?

- I still can’t figure out how Mulder managed to survive that accident, let alone walk around as if nothing happened within a few hours!

- Why would Scully just drop her concerns about Mulder’s obsessive reckless behavior, and bring up the shoe?

- Why would Bill Mulder contact his son through Skinner? Aren’t the basement phones or voicemail working? Of course, then Mulder wouldn’t know that something had brought his parents to the same place...

- How many places does the street number have to be displayed in Germantown, MD?

- Could Bill Mulder be any more unsettling?

- Bill keeps that house in damned good shape...

- Scully looks damned good with her hair pulled back like that!

- Interesting how Scully ignores the sight of a dying, non-human fetus in an alien-looking sack...

- Why wouldn’t Scully take her cell phone into the bathroom, if she knew that Mulder’s call would be important?

- There’s that 11:21 again...

- The bounty hunter isn’t shown with the ability to alter his clothing with his appearance, so where is he getting the perfect outfits to impersonate people, if he’s not killing all of them first?

Overall, this episode is one of the most influential early entries in the mythology. Though later revelations regarding elements of the episode would make deciphering its events nearly impossible, it stands as one of the first “event” episodes in the course of the series. Only some minor plot conveniences take away from its quality.

I give it a 9/10.

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