The X-Files Colony and End Game: Why the Alien Bounty Hunter Two-Parter Still Stands Out

Colony and End Game, the two-part story from the second season of The X-Files, is the best run of UFO mythology episodes the show had produced up to that point. It introduces one of my favorite characters, the shape-shifting alien bounty hunter, and it brings back Mulder's sister.

The X-Files, starring David Duchovny and Gillian Anderson, began its second season on September 16, 1994. It's the longest season of the series, with 25 episodes, and it arrived almost exactly a year after season one. I feel this is the season where it went from a cult hit to a cultural phenomenon, and "it can't be overstated how important this season was." They filmed, wrote, edited and released almost 50 episodes in two years, which makes you wonder how we got to the point of eight episodes every two years. Real world issues also shaped production: Anderson became pregnant around that time, so several storylines were changed and it was decided that Scully would be kidnapped by aliens.

Brian Thompson's alien bounty hunter is the most intimidating character in The X-Files

This two-parter pushes deep into the UFO mythology. Alongside the bounty hunter and the return of Samantha, we get confirmation of humans being injected with alien DNA. The bounty hunter is played by "the unforgettable Brian Thompson," who is a standout in the series. Growing up, I wasn't interested in the UFO episodes, but I always remember reacting with alarm whenever he arrived.

I feel the writers learned from killing off an earlier villain and decided that a recurring killer who doesn't die on his second appearance was a smarter way to go. As a kid I thought he was like Arnie in The Terminator, and I did wonder if they cast Thompson because of his look. He's an unstoppable assassin who bleeds green toxic blood, so if you shoot him, you only hurt yourself. The only way to kill him is to pierce the base of his neck, which means getting up close to a seven foot man built like a bodybuilder. Thompson plays by far the most intimidating character in the show, and yes, I will forgive him for Mortal Kombat Annihilation.

The character was originally supposed to be an alien pilot. Thompson was told to get a crew cut, but he showed up with a different hairstyle and said there must have been a misunderstanding. The producers liked the look, and that's how the character stays throughout the series.

Colony opens with a frozen Mulder and a string of identical murdered doctors

Colony begins with Mulder's body in bad shape and Scully rushing to the doctor who returns from the episode Firewalker. Mulder is freezing cold, and while the medical staff want to warm him in a bath, Scully demands he be kept at that temperature. The episode then jumps back two weeks, to a boat rescuing the bounty hunter after his ship lands in the Beaufort Sea.

He travels to Pennsylvania and kills a doctor at an abortion clinic, thrusting a sharp, needle-like object into the back of his neck. Green blood pops out. A couple of days later, Mulder receives the obituary along with those of two other identical-looking doctors. A fellow FBI agent sent to find one of them arrives to see him being murdered, shoots the bounty hunter, and the green blood makes his eyes flare up. The bounty hunter then takes his face and tells Mulder and Scully the doctor wasn't home. When the real agent's body turns up, Skinner decides there's too much murder and too much weirdness, and closes the case.

Mulder is then contacted by a CIA agent named Ambrose Chapel, who says the doctors are clones, building off the plot of Eve from season one, or so we think. He says they're being targeted by the US and Russian governments because of what they know, and that this has been going on for decades. When Mulder, Scully and Chapel reach another doctor's house, the doctor panics at the sight of Chapel, because Chapel is the bounty hunter. The doctor throws himself out of a window, but Chapel catches and kills him. Scully steps in green blood, starts to suspect Chapel isn't who he says he is, and later finds him destroying the lab where the doctor worked.

Samantha Mulder's return and the Colony cliffhanger

Meanwhile, Mulder's parents call him home. His father was mentioned last season, but this is the first time we meet him properly. Waiting with them is Samantha, who seems completely healthy. On the surface, everything checks out. She says she was abducted as Mulder remembers, returned to Earth around the age of nine or ten, and given to an adoptive family who were apparently visitors to Earth. Her memories were repressed, and only in adulthood, when anxiety led her to therapy, did she remember everything under hypnosis and come home.

It's devastating, because her family believes she's back and you see their relief at never having given up hope. Her mother even says that after all her sleepless nights, she can't believe she can't stay awake. In hindsight, that makes it more devastating, because they all clearly want to believe. Samantha tells Mulder the hunter has finished off most of the clones and will now come for her and her parents. He can look like anyone, but she says she can recognize him.

Scully, calling Mulder from a bus, says she's sure she hasn't been followed and names her motel, as the camera pans out to show the bounty hunter two seats away, not even in disguise. She finds the final four clone doctors, who are taken to a jail, where the bounty hunter arrives in disguise and kills them. Then comes the ending. Mulder knocks on Scully's motel door, she lets him in, and just as she feels safe, her phone rings with a call from Mulder. I remember this being shown on TV to promote the show. It's a cliffhanger and probably one of the series' best moments. I can imagine waiting a week was agonizing. It's such a good episode, and in my opinion "the best of the UFO ones so far."

David Duchovny's story idea and the meaning behind the Colony title

This was Duchovny's first credit as a story writer, as he came up with the idea of an alien bounty hunter. The idea was then tied into his sister so that it could build the overall mythology. The actress playing Samantha does a fantastic job, and they struck gold with the casting. She has a meek, girl next door quality.

As for the title, it turns out aliens have been here for a while and are planning to build a colony, mixing alien and human blood to create hybrids that can look like anyone. The doctors worked at abortion clinics because they'd have access to fetal tissue to advance the hybrid race. Meanwhile, purebred aliens are disgusted by the idea of their kind mixing with humans, which is why the bounty hunters come to clear things up.

End Game raises the budget with the USS Allegiance and a hostage exchange

End Game sees the budget skyrocket. It opens with the atomic submarine USS Allegiance in the Beaufort Sea, which comes across the alien ship. The craft disables the sub and strands it in the ice, setting up the rest of the episode.

Back at the motel, Scully stands up to Mulder and tells him to face the wall. He's confused but cooperates. I'll admit I was anxious watching it, unsure which Mulder was real, even though I'd already seen it. He reaches for his ID, takes her down and reveals he's the bounty hunter. Mirroring her kidnapping by Duane Barry, Scully is taken again, and the bounty hunter offers to trade her for Samantha. Mulder isn't happy, but Samantha agrees, seeing it as their best chance to take him out.

At a bridge, sharpshooters surround them, and one fires while Samantha and the killer are wrestling. Both go into the river, and the search team can't find them. Mulder's father has a heartbreaking scene where he's clearly devastated that Fox has lost Samantha again, and he lays into his son harshly, though, as later seasons reveal, I'm not sure he should be saying that. Bill says Samantha gave him a note about where to meet if they were separated, which leads Mulder to a clinic.

The Samantha clones and Skinner's fight for Mulder's whereabouts

Scully calls with bad news: Samantha has washed up on the shore and died. Mulder is devastated but heads to the clinic anyway, and Samantha's body starts disintegrating into green blood. At the clinic, Mulder finds clones of Samantha, who reveal they sent a duplicate and that the real Samantha is here. The bounty hunter arrives, burns the place down and seemingly kills all the clones. Devastated, Mulder meets X, who tells him about the sub and says the answers will be there.

Mulder goes AWOL, and Scully searches for him with Skinner. There's a hilarious scene where Scully finds X at Mulder's apartment, and he plays dumb the whole time, with a good poker face that is also very suspicious. Skinner doesn't put up with it, and the pair fight in a lift, which is how he gets Mulder's whereabouts. It's a great scene for Skinner and shows that, when it comes down to it, he has the agent's best interests at heart and will get his hands dirty. Scully also learns that anyone exposed to the virus must stay cold, because the temperature wipes it out and lets the body fight it off.

The submarine set and Mulder's renewed hope in End Game

Mulder reaches the sub in the Arctic. A sequence like this had been on the crew's wish list for a while, and they'd wanted to do something similar for the episode Ice but didn't have the budget. They used the interior of HMCS Mackenzie and brought in 140 tons of snow to create the set, and the sub was later reused in another episode. It's an iconic set, and the top of the sub popping out of the ice has always stuck with me.

Mulder finds what seems to be a surviving crew member, but quickly realizes it's the bounty hunter. The hunter says he could have killed Mulder several times, but Mulder ignores that mercy and shoots him in the back, exposing himself to the blood. He begs to know whether Samantha is alive, and the hunter says she is before throwing him out of the sub. As it sinks, Mulder is almost cut in half by a diving plane, but he's rescued, bringing us back to Scully insisting he be kept cold.

Though it's a sad couple of episodes, with Samantha's return revealed as a trick, the story ends on a more hopeful note. From his hospital bed, Mulder says he's regained something he thought he'd lost: the hope of finding his sister. The bounty hunter's words have renewed his faith, and he will keep believing. It tops off a set of the strongest episodes in the show so far.