Written by Frank Spotnitz
Directed by Rob Bowman

In which Mulder discovers the truth about his sister’s apparent return, forcing him to go to extreme lengths and risk everything to hunt down the killer and learn the truth...

Synopsis - Analysis - Memorable Quotes - Observations




As the episode begins, the USS Allegiance nuclear submarine cruises beneath the ice of the Beaufort Sea, 67 miles north of Deadhorse, Alaska. The captain is informed by the radar officer that something has been detected just under the ice, emitting radio signals in what appears to be a random pattern. The captain calls Naval Command for orders, and is shocked by what’s he hears. Hanging up, he orders his crew to prepare to destroy the object. The radar officer objects, but the captain insists that his orders be followed. Without warning, a sudden burst of high-pitched noise fills the submarine, and within seconds, the submarine is reduced to battery power. With no other options, the captain orders his crew to head for the surface.

Meanwhile, at the Vacation Village Motor Lodge, Scully hangs up on Mulder, pretending that it’s a wrong number. She pulls a gun on the bounty hunter, even though she has no idea who or what is pretending to be Mulder. The bounty hunter plays along, claiming to be Mulder and dismayed at Scully’s behavior, until he gets a chance to grab Scully’s gun and send her flying into the wall. The bounty hunter demands to know where Mulder is, and smashes Scully through a glass table for good measure.

Shortly, Mulder and Samantha arrive at Scully’s room. Scully is gone, and the room is in shambles. Samantha is positive that it’s the work of the bounty hunter, and that he’s keeping Scully alive so he can exchange her for Samantha. On the way back to the car, Samantha explains that the bounty hunter can only be killed by a precise strike to the base of the skull. However, the bounty hunter is so advanced that Samantha can’t be sure that the method will work on him. Even worse, if the method doesn’t work, exposure to the hunter’s blood is toxic. To Mulder, it all makes a kind of sense.

That night, after midnight, Mulder and Samantha anticipate a call from the bounty hunter. Mulder begins to wonder if Samantha is really telling him the truth, accusing her of holding things back. Samantha reluctantly explains that the Gregors were the cloned progeny of two original visitors who arrived on Earth in the late 1940’s. The clones have been trying to establish a colony, under the belief that humanity will eventually perish, leaving the colony as the heirs to the planet. Meanwhile, through genetic hybridization experiments, the colony has been seeking ways to expand the gene pool. However, the bounty hunter was sent because the experiments were considered a “dilution of the species”.

Before they can continue discussing details, there’s a knock at the door. Fearing that it’s the bounty hunter, Samantha grabs an ice pick and hides in the shadows of the kitchen. The man at the door identifies himself as Skinner. Mulder tells Skinner to come in. Skinner comes in, but the lights are off, making it hard to see. Skinner says that he’s been trying to reach Mulder and Scully regarding the disappearance of four men in federal custody.

Samantha steps into view, declaring that Skinner isn’t the hunter. Skinner is justifiably confused, so Mulder introduces Samantha as his sister. Skinner becomes justifiably shocked. Mulder continues, telling Skinner that Scully is missing, but the phone rings before he can fully explain. It’s Scully, and she’s being held by the hunter. Scully tells Mulder that the man holding her wants the woman with Mulder, and the man wants to trade in one hour at Memorial Bridge at Bethesda.

After quickly updating Skinner on the situation, arrangements are made to take down the hunter at Memorial Bridge. Mulder and Samantha drive up to the bridge, with Skinner and a sniper waiting nearby. Another car pulls up from the other side of the bridge, and the hunter gets out with Scully, holding a gun to her head. The hunter demands that Samantha walk towards him, and as soon as she’s in range, the hunter pushes Scully away and grabs Samantha. Samantha tries to attack the hunter with the ice pick, but fails. Her efforts drive the hunter into a spot where the sniper cannot get a clear shot. Mulder advances, and as soon as the hunter steps into view, the sniper takes a shot. The hunter staggers to the side, toppling over the side of the bridge…taking Samantha with him.

By morning, there is no sign of either the hunter or Samantha. Scully arrives on the scene to check on Mulder, who is still in shock at losing his sister. He still holds out hope that if they recover her body, she might somehow be revived. Scully wonders if Samantha might have been a fake, like the hunter had been, but Mulder angrily denies the possibility. Mulder leaves, explaining to Scully that the hunter is an alien, and that now he has to face his father with the knowledge that Samantha is gone…this time for good.

Bill Mulder comes to Mulder’s apartment, and Mulder immediately tells his father that Samantha is gone, that he let a man holding his partner hostage take his sister away. Mulder takes full responsibility. While Bill seems upset about the news, he seems more concerned about how Mulder’s mother is going to take it. Mulder tells his father that he’s sorry, but Bill just drops an envelope onto the nearest table, explaining that Samantha left it at the house for Mulder. Bill leaves without another word, leaving a tearful Mulder to look at the contents of the envelope. Inside, Mulder finds a keycard and a letter from Samantha, telling him to meet her at a specific address if anything should happen to her.

Mulder follows the directions to a women’s health clinic in Rockville, Maryland. Outside, he gets a call from Scully. Despite his hopes, Scully delivers the bad news: Samantha’s body has been found. The body of the hunter is still missing. Mulder promises to get there as fast as he can, but enters the clinic anyway. Meanwhile, back at the bridge, another agent grabs Scully. They run to where Samantha’s body was taken, and watch in awe as Samantha appears to dissolve into a mush of green goo.

Mulder enters the clinic, and finds a woman in scrubs standing at a desk. Mulder pulls a gun on her, demanding to know who she is. When she does turn around, Mulder is stunned to see another Samantha, staring him in the face. The other Samantha tells Mulder to follow her into another room, and when he finally consents, he finds yet another Samantha waiting for him. Realization dawns, and he realizes that his sister never returned. The remaining Samanthas beg Mulder to save the original Samantha, not believing that the hunter is dead. Disgusted by the manipulation, Mulder refuses.

Without warning, a fire alarm begins to blare. The Samanthas are sure that the hunter has come, so Mulder begins finding his way out, gun in hand. The hunter waylays him, however, leaving him unconscious on the floor. Moments later, a fireman finds Mulder among the flames, and pulls him out. Mulder insists that the firemen go back for the women, but of course, they tell him that no one else survived.

Back in Washington, Scully drafts her report. Mulder insisted on having the remains of the clinic searched, but no evidence was found. There seems to be no explanation for the identical men and women, since Mulder’s claims of alien origin cannot be substantiated. The bounty hunter is still at large. Study of Agent Weiss’ body (killed in “Colony”) reveals the presence of a retrovirus that causes the body to overproduce blood cells, leading to death. Further study of the retrovirus demonstrated that a minor reduction in temperature inhibited the growth of the virus. Scully notes that the cold of the water kept Samantha’s body intact, but as soon as it warmed, it began to “corrode”.

Mulder meets with his informant, seeking help in finding the hunter. The informant tells Mulder that the hunter’s craft was located five days earlier by a nuclear submarine. An attack fleet is on the way to make sure the hunter does not leave. Mulder insists on being given the chance to get there first. The next day, Scully stops by Mulder’s apartment, and he’s gone. She checks his computer, and finds a message waiting for her. Mulder tells her that he had to take care of the matter on his own, without risking her life for his personal need for answers.

Scully goes to Skinner, hoping that he can use his connections to “unofficial channels” to determine where Mulder was going. Skinner rejects Scully’s request, explaining that Mulder made his choice, for himself and for everyone else. Scully returns to Mulder’s apartment, and finds a taped “X” on the window. Figuring out what it’s for, she shines Mulder’s desk light on the “X” and waits. Sure enough, later that night, the informant knocks on the door. When he sees that it’s Scully, the informant turns and walks away, denying any knowledge of Mulder.

The informant takes the elevator, but when the doors open, Skinner is there to confront him. Skinner tries to beat the necessary information out of the informant, but the informant gets the upper hand. Still, Skinner makes it clear that Mulder’s survival depends on getting the information. Skinner shortly shows up at Mulder’s apartment, coordinates in hand.

Mulder arrives at those coordinates, where a conning tower has broken through the ice. Mulder climbs into the submarine, and finds a number of dead men throughout the corridors. Hearing movement, Mulder chases after it, and finding a frightened man. Mulder forces the man to explain what happened. The man says that someone came, sealed everyone below decks without air, and killed the stragglers. The man claims to have survived by playing dead, but Mulder doesn’t believe him. He handcuffs himself to the man, demanding to know where his sister is. The hunter drops his ruse, and proceeded to toss Mulder around by the handcuffs like a rag doll. Mulder insists on being told where his sister is. The hunter, tired of the game, tells Mulder that his sister is alive.

Mulder manages to get his gun, and he tries to shoot the hunter in the back of the neck. He misses, and becomes overwhelmed by the retrovirus. The hunter quickly takes Mulder to the top of the conning tower, pushes Mulder out, and slams the hatch shut on the extended chain of the handcuffs. The chain breaks, and Mulder plummets down onto the ice. Stunned and battered, Mulder barely dodges the fins of the conning tower as it descends.

Sometime later, Mulder is rushed into the emergency room at Eisenhower Field, exactly as depicted in the beginning of “Colony”. Scully argues with the doctor, insisting that Mulder will die from a lethal retrovirus if his body temperature rises. Sure enough, Mulder’s vitals plunge, until Scully gets him out of the warm water bath and revives him with a defibrillator. It works, and Scully begins the long process of saving Mulder’s life.

Scully’s report details how an aggressive treatment of blood transfusions mixed with powerful anti-viral agents resulted in a slow but steady improvement in Mulder’s condition. The search for the submarine, the supposed hunter, and the hunter’s vessel has been completely unsuccessful. Scully is convinced that there must be a scientific explanation behind what happened, even if it hasn’t been found. After all, it was science that provided the information necessary to save Mulder’s life.

Scully visits Mulder as he recovers, and Scully explains that a recon squad from the attack fleet found Mulder and rescued him. Mulder apologizes, explaining that he couldn’t risk Scully’s life. She asks if he found what he was looking for. Mulder admits that he did not…but that he regained faith to keep looking.


This episode takes many of the layered circumstances of “Colony” and gives them context, something which would become exceedingly rare as the series marched on. Contrast the relatively clear plot threads of this two-part episode to the mythology of the last four seasons, and there is a noticeable difference in the strength of the character and plot arcs from beginning to end. Having set up the central conflicts in “Colony”, Carter and Duchovny leave the resolution in the hands of Frank Spotnitz.

From the teaser, there are hints of something bigger than what is revealed in this episode. It’s clear that the hunter was sent on a specific mission, since his vessel is either manned by someone else who recognized that the submarine could be utilized for the hunter’s return, or it was programmed to search for such a thing on its own. Either way, the hunter is not there to take his time; this is a surgical strike.

The hunter is also well aware of Mulder and Scully’s relationship, and Mulder’s history of doing whatever it takes to ensure Scully’s safety. Certainly, “One Breath” takes place about three months earlier, so it’s possible that the hunter was aware of those events. However, one would think that the conspiracy would have kept those events under a cloak of secrecy, and since the hunter is clearly at odds with the conspiracy, that means that the hunter’s employers had to have another source of information. Both the surgical strike and knowledge of Mulder’s history fits within the theory that the hunter is related to the future rebellion (as discussed in “Colony”).

The Samantha clone mentions that the hunter has abilities that surpass what she is familiar with. She also tells Mulder another one of her “lies hidden within truth”. It is later revealed that the conspiracy began with the events at Roswell in 1947, where it is said that as many as two living aliens were recovered. Samantha’s explanation would appear to suggest that the original Gregor and Samantha were recovered at Roswell, and that they eventually began the work that yielded the cloning experiments of the 1950s (“Eve”) and the later hybridization and genetic experiments.

If the eventual schism between the organic super-soldiers occurred before the experiments could progress to the level of the hunters, then it would suggest that the stage during which Gregor and Samantha were created might have been early enough that the crash at Roswell could have been from clones created by either side of the conflict.

However, as later seasons demonstrate, while both the conspiracy and the rebellion became obsessed with genetic purity, only the rebellion elevated that obsession to cult status. One purpose of the organic super-soldier experiments was to artificially create a child with a specific genetic code, discovered on what was thought to be an ancient UFO inscribed with prophecy.

But the UFO that crashed at Roswell, in terms of the folklore, also had strange writings and markings inscribed in the metal. Therefore, it is likely that both the ancient UFOs (seen in “The Sixth Extinction” and “Provenance”) and the Roswell UFO came from the same group, one that had elevated a specific genetic code to almost messianic status.

If the inscribed UFOs were used by the rebellion, which rejected the attempts by the conspiracy to evolve to the completely non-corporeal intelligence of the black oil virus, then the original two survivors of the Roswell crash were the product of rebellion experiments. Since the conspiracy was necessary if the organic super-soldiers were to exist, and the Gregors and Samanthas would have been needed to begin and perpetuate the experiments towards that goal, a sinister plan becomes clear.

The rebellion sent the hunter to eliminate the Gregors and Samanthas, which they themselves sent back to ensure that specific experiments were conducted. When the experiments went as far as necessary, the hunter was sent to prevent further experiments, which would have introduced genetic components which could not be allowed to exist. The hunter was then to return to the future without being caught, to prevent the conspiracy from learning about the rebellion.

It’s clear that the bulk of the conspiracy was unaware of the rebellion until a specified time. It’s even more clear that some original members of the conspiracy knew exactly what was happening, and kept the truth to themselves. One of them had to be the cigarette-smoking man. After all, CGB Spender knew that Mulder possessed key genetic similarities to the genetic information recovered at Roswell, and purposefully kept Mulder close to the conspiracy and alive. However, it is equally clear that if Spender knew the truth from his knowledge at Roswell, then certain decisions made in 1973 suggest that someone else was aware of the truth: William Mulder.

Throughout this episode, it is clear that Bill Mulder knew that Samantha was not Mulder’s sister. His reactions, especially when Mulder confesses to losing Samantha again, prove that theory on their own. In “Colony”, Bill Mulder kept Samantha at a distance, having already seen the original decades earlier and during his work in the conspiracy. No longer a part of that conspiracy, he couldn’t know why Mulder and his mother were being manipulated, but he would have been well aware of the emotional scars that would be reopened.

That explains why Bill Mulder simply wants to know what happened to the Samantha clone, and then focuses on the consequences for Teena. Bill understands that it was the loss of Samantha in 1973, and her completely unexplained disappearance in 1979, that has haunted Teena ever since. Unlike Bill, however, Teena wouldn’t know that Samantha wasn’t really her daughter. He would have only known that the clone was using the family, and that he would have to conduct the damage control.

This brings the end of the episode into question. It’s clear from the perspective of this theory that the hunter does everything possible to keep Mulder alive while also carrying out his mission. Considering how many other people are killed along the way, there has to be a specific reason for the hunter to preserve Mulder’s life. The hunter goes out of his way to get Mulder out into the cold, aware of the effect of the retrovirus. It stands to reason, then, that the rebellion is aware of Mulder’s genetic profile, and that he must survive to father William.

But why, if the hunter knows the history of the conspiracy and Mulder’s family so well, would he tell Mulder that his sister was still alive? There are two answers. The first is obvious: based on his delivery and tone, he was telling Mulder what he wanted to hear, so he would regain his faith to keep looking and fulfill his destiny.

The second possible answer relates to the spiritual side of the universe in which “X-Files” takes place. It’s clear that there are non-corporeal intelligences at work, and that they have their own agenda that runs counter to both the conspiracy and the rebellion. It is likely that those same intelligences were behind the disappearance of the real Samantha in 1979, as shown in “Closure”. The organic super-soldiers like the hunter, possessing a primitive non-corporeal intelligence of their own, would not see a conversion from flesh to coherent spirit as “death”. Rather, the real Samantha is still very much alive…only in a different way than Mulder can understand.

The truth, of course, is probably a combination of both and much more; that’s part of the appeal. Rather than view what is shown in “Closure” as a contradiction to what is shown here in “Endgame”, it can be even more intriguing to consider that there is a consistent explanation for both. Not that it was necessarily intended; after all, the “official mythology” of “The Truth” fails to address even the most obvious of contradictions. Given that the series is all about the fallacy of “official” truths, should anything less be expected?

The very end of the episode is interesting, because while Scully’s conclusions are completely consistent with her second season personality of denial (rather than simple disbelief), Mulder’s admission doesn’t make quite as much immediate sense. Mulder was supposed to have lost faith after the X-Files were closed and he was reassigned, and the events of “Little Green Men” were supposed to reinvest him in his crusade. Why, then, would he still be looking for “faith to keep looking”?

One possible answer is that he realized, in the wake of Scully’s abduction, that the events in “Little Green Men” were largely staged by the conspiracy. After “One Breath”, Mulder would have had more than enough reason to believe that he would never find the truth. But now, he knows that there are forces at work beyond the conspiracy, since his informant made it clear that the military was trying to capture the hunter themselves.

Unlike the later seasons, where character development for Skinner would become a rarity at best, this season thus far demonstrates a clear path from unwavering tool of the conspiracy to a man conflicted between his fear of those behind “unofficial channels” and the desire to discover what those powers are hiding. Skinner becomes a strong example of Mulder’s ability to influence others to take up his crusade.

While the conspiracy at large might have wanted Mulder’s involvement in protecting their resources, it’s clear that Cancer Man wanted that involvement to be limited. The informant makes it clear that Mulder is not meant to be involved once the clones are destroyed, but once it’s clear that Mulder will refuse to back down, the informant struggles to preserve Mulder’s life while still protecting the aims of his employer. The deciding factor, in the end, has to be the first stirrings of sympathy for Mulder’s crusade…a common failing among Cancer Man’s underlings.

One of those rare combinations of strong plot and character threads, “Colony” and “Endgame” manage to continue the fine tradition of the mythology as depicted in the abduction arc. However, there are also the first stirrings of an intentional ambiguity, and unlike the lengthy continuity of the abduction arc, this epic is surrounded by stand-alone episodes that don’t mesh very well with the events depicted. This would become the norm for the series, breaking down what had been a stunning bit of cooperative writing.

Memorable Quotes

HUNTER: “If I wanted to, I could’ve killed you many times before.”
MULDER: “Where is she?”
HUNTER: “Is the answer to your question worth dying for? Is that what you want?”
MULDER: “Where is she? Just tell me where she is!”
HUNTER: “She’s alive. Can you die now?”

SCULLY: “Did you find what you were looking for?”
MULDER: “No. No, but I…I found something I thought I’d lost. Faith to keep looking.”


- Love that opening music in the teaser...incredibly evocative, especially given the importance of this early episode in the mythology...

- Gee, that noise just about disrupted me, let alone the submarine!

- I love David’s face when he’s playing the hunter...you can tell he’s been taking Terminator lessons...

- That comment about the “powers I’ve never seen before” provides a nice explanation for the ability of one of the hunters to recover from a pick to the neck in “Herronvolk”!

- It’s amazing that Mulder questioned Samantha’s honesty only once...

- Skinner takes Mulder’s odd behavior a little too calmly, especially given the circumstances!

- Skinner must think that Mulder is really bad at keeping tabs on partners, or getting them taken hostage...

- Why only one sniper? Wouldn’t coverage from the opposing angle have been more intelligent, given that the shot has to be the back of the neck? Then the shot could have been taken almost immediately!

- Seeing Bill Mulder’s continually tight expression, is it any wonder that Mulder seems to have only a handful of facial expressions?

- David Dachovny should just stop trying to cry...it looks really bad...

- Why didn’t Scully call Mulder as soon as she saw what happened with Samantha’s body?

- I don’t suppose needing a keycard to get into a largely abandoned and mothballed building didn’t set off Mulder’s warning signals at all...

- Note that only a minor change of temperature is required to inhibit the retrovirus, while a much lower temperature is needed to control the activity of the black oil virus...

- How can all of this take place in two weeks? Just going by the time frames indicated in “Colony” and “Endgame”, the time required is more like three weeks!

- Skinner’s head-butt looked like it was more of a face plant...

- Exactly where is that light coming from behind the conning tower, and what about the stars? Yes, indeed, that ice shot looks incredibly fake!

- Regardless, it is one hell of an image...

- Given his earlier experience and information on the hunter, why would Mulder be foolish enough to handcuff himself to the thing?

- There’s no way that Mulder could have rolled that slowly out of the way, if that close-up shot was supposed to be his perspective!

- Exactly what made the ER doctor suddenly accept Scully’s version of events? And exactly what was that actor’s deal with the words “body heat”?

Overall, this is a solid second half to “Colony”, one of the rare episodes that actually does justice in resolving a previous episode’s main challenges. There’s a lot of subtle character work in this episode, but at the same time, the mythology is still relatively cohesive to this point. The later seasons would wipe much of the promise out with needless complications, but the end of this episode gave the audience just as much faith as Mulder.

I give it a 10/10.

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