episode written by Frank Spotnitz
summary written by Pellinor
Internal dating: Mulder goes to the submarine at the end of "End Game" on February 3rd 1995 - which is the time shown in that global positioning thingy. The story told in "Colony" begins two-weeks earlier, as we are shown on screen, placing it neatly as around January 20th or so - rather close after "Die Hand". There are a few nice nit-picky mistakes, though. At the start of "Colony" Mulder and Scully are investigating the recent death of Doctor Landon Prince of Scanton. Close inspection of Mulder's e-mail reveals that Prince was killed on December 28 1994. Unfortunately, it also reveals that another of the doctors, Harvey Buchanon, was killed on January 10 1995, despite the fact that Mulder calls Prince the "latest victim." Oops.
Beaufort Sea, Alaska. A US submarine comes across a strange craft beneath the ice. It is emitting radio signals. To the captain's dismay, the admiral orders them to fire on it. Suddenly something destroys all their electrical things and they have to surface, although they are under thick ice.
Continuing where Colony left off: Scully hangs up on the Mulder on the phone, telling the Mulder in her room that it was a wrong number. She then pulls a gun on him and orders him to face the wall. He protests innocence and confusion, but then turns round and hits her. "Where is he?" he asks, morphing into the form of the Bounty Hunter. Mulder and Samantha get to Scully's room and find it trashed, with no sign of Scully. Samantha assures him Scully will be okay. She was taken to be traded for her, because she knows how to kill him, by piercing the base of his neck. She also says that his blood is fatal to humans.
Later (12.38) Mulder's anxiously pacing his apartment. He's beginning to have doubts about the whole thing. "After 22 years why come back?" he asks, complaining that Samantha's told him only what she had to, telling him next to nothing about the doctors. She says the doctors are clones who've been attempting to set up a colony since the late 40s. They have to live apart as they're identical, but by hybridisation, using foetal tissue from the abortion clinics, are managing to make it so they appear different. "Though the biologies are incompatible, they've finally found a way to combine human DNA with alien DNA." They believe that humans are forfeiting their stewardship of the planet and they will step in. The bounty hunter is killing them because the project wasn't authorised, and is condemned as a dilution of their blood.
"That's a good story," says Mulder, "I've heard a lot of good stories lately." "I've got no reason to lie to you," Samantha says, "I'm your sister, Fox. You've got to trust me." Then there is a knock at the door.
Skinner comes in to find Mulder sitting in the dark, singularly uncommunicative. Suddenly the lights go on and Samantha comes out with a knife, but she says "it's not him." Mulder introduces his sister to a confused Skinner, when the phone rings. It's Scully, with blood on her head, calling from a call box. She says the bounty hunter wants Mulder to meet at the Old Memorial Bridge in Bethesda in an hour, bringing "a woman who's with you", whom he'll trade for her life. Mulder wants more time to negotiate but the Bounty Hunter cuts off the call. Mulder turns to Skinner. "If I ever needed your help - your trust - I need it now."
One hour later, Mulder pulls onto the bridge. Skinner and a sharp-shooter watch from below, intending to shoot the Bounty Hunter as the trade is being carried out. Scully is pulled out of the car and the trade proceeds, but a bridge support gets in the way and the sharp shooter can't shoot. "Scully, are you alright?" Mulder asks several times as she runs past him to the car, while Samantha is being grabbed. As Scully cowers in Mulder's car, Samantha tries to stab the bounty hunter and the shooter shoots, but the bounty hunter, with Samantha, topples off the bridge. "Samantha!" Mulder shouts into nothingness, as Scully looks on in horror.
Next morning, Mulder is still at the bridge, watching as they drag the river for bodies. Scully drives up, having been discharged from the hospital. Mulder hopes Samantha's still alive, having heard of people who've survived for ages due to hypothermic shock. Scully isn't hopeful. She asks him why he hadn't told her it was Samantha. "I couldn't tell you," mutters Mulder, not looking at her. "Because you'd never let me go through with it." Scully asks him if he's sure it was Samantha, saying how the bounty hunter at the motel had looked just like him. "It was her," Mulder shouts, walking away. Scully asks who the man was. "He's an alien," Mulder interrupts. He says he's already told Skinner this, and now he's got to do the hardest thing - tell his father.
Mr Mulder comes to Mulder's door. He doesn't come in. Mulder turns away, unable to speak. "Samantha's gone, Dad," he mumbles, scarcely coherent. "I lost her." He tries to explain about the situation, but Mr Mulder is very stern and unforgiving. "You let this man take your sister. Isn't that what you're trying to tell me?" Mulder is close to tears. "I believed I was doing the right thing." "Was this your decision?" his father asks. "Yes" says Mulder. Mr Mulder demands to know if he realises what this will do to his mother. Mulder is crying, aplogising over and over.
Before he goes, Mulder's Dad leaves him a note from Samantha. It contains an entry pass for a women's clinic where he was meet her if they get separated.
Mulder goes to the clinic. Scully calls and he tells her he thinks Samantha's alive, but Scully tells him they've just found her body. "Whatever you're feeling, you can't blame yourself," she tells him.
As Scully watches, Samantha's body corrodes into a green mass.
Mulder goes into the clinic, finding a four women who look just like Samantha. They are tending green vats of liquid. "It was all a lie," says Mulder. "We needed your help. We knew you could be manipulated," they tell him. They say the Bounty Hunter will be coming, even though Mulder says he's dead from falling off the bridge. They say one of their number is the original and has to be protected. Mulder refuses to help. "My choice is to walk out of here," he says. They say they know where his sister is - how else would they have known so much about her?
The alarm goes off and the Bounty Hunter comes in, knocking Mulder out and burning the place. Mulder is rescued later by the fire fighters, who say no other bodies were found.
Next day, Scully is writing her report. She says many aspects of the case still defy explanation. Agent Weiss' cause of death is now listed as a unknown retrovirus. A scientist analysing it shows Scully how the virus goes dormant at cold temperatures. Scully wonders if that's why "Samantha's" body corroded after coming out of the cold water.
Mulder meets X outside the opera, demanding to know more. X is unhappy with the meeting and doesn't want to talk, but Mulder insists. X tells how the Bounty Hunter's craft is in the Arctic and a fleet is being dispatched to stop him leaving. Mulder wants to go there, "You'll only win the war if you pick the right battles," warns X. "This is a battle you can't win."
Two days later, Scully goes to Mulder's apartment, finding several newspapers on the doorstep. On his computer she finds a letter to herself from him. "Scully, when you get this message I'll be too far away for you to stop me, but where I'm going I can't allow you to follow. I won't let you jeopardise your life and your career for reasons purely personal to me. You were right, Scully. You said a line has to be drawn somewhere. I'm drawing it for you here. I'll contact you when I can."
Scully goes to see Skinner, asking if she can speak off the record about Mulder. She wants him to help her find Mulder, through "unoffical channels" if necessary. Skinner says he and her have to consider their duty to the FBI, which Mulder has neglected. Scully protests that Mulder has saved her life in the past, but Skinner refuses to help, saying Mulder would have told her if he'd wanted her to know.
Scully goes to Mulder's apartment and sees the X in his window. She shines a light through it and settles down to wait. Much later, X knocks on the door, but when Scully opens it he walks away, saying he got the wrong room. "Where's Mulder?" she demands, running after him. "I'm losing time."
X refuses to help Scully but when he gets out of the elevator he meets Skinner. The two men fight, until X pulls a gun. "I've killed men for far less," he says. Skinner says if he pulls the trigger he'll be killing two men.
Skinner shows up at Mulder's door and tells Scully where he is (in Alaska). He's bloody and dishevelled. "Unofficial channels," he says, when Scully asks him how he got the answer.
In the Arctic, Mulder finds a submarine conning tower which has punched through the ice. Inside he finds one terrified man. The man explains how he's the only survivor after a man came and started killing everyone. He hid under a body and wasn't seen. Mulder doesn't trust him and handcuffs himself to him, holding a gun to the base of his neck. He's sure it's the Bounty Hunter. "Just tell me how I can find her and I'll let you get back to your ship before it's destroyed!" he shouts, referring to Samantha. "Please," the man whimpers. "You're making a terrible mistake." But as he says this he morphs into the Bounty Hunter and throws Mulder to the floor.
Mulder is thrown around painfully. "Where is she?" he asks over and over. "She's alive," the bounty hunter says at last. "Can you die now?" As Mulder's dragged along by his handcuffed wrist, he manages to reach his gun and shoots at the back of the alien's neck, but then starts crying out in agony. Mulder's dropped onto the ice where he's nearly crushed as the submarine submerges, but manages to roll away just in time.
We now return to the teaser of "Colony". Mulder's heart has stopped, and the ER doctor isn't at first willing to listen to Scully's insistence that Mulder should be kept cold, due to the retrovirus. Eventually he allows her to take over, and she gets Mulder's heart started again.
As Mulder slowly recovers, due to transfusion and anti-viral agents, Scully says, in voice-over, how there are still certain unexplained elements about this case, but it has only strengthened her desire to find answers in science. "Many of the things I have seen have challenged my faith and my belief in an ordered universe, but this uncertainty has only strengthened my need to know - to understand - to apply reason to those things that appear to defy it." It was science, she says, that saved Mulder's life by isolating the retovirus.
Mulder stirs at last. "Thanks for ditching me," Scully says, though she's smiling broadly at the sight of Mulder conscious, Mulder apologises, explaining how he couldn't let her risk her life. Scully asks if he's found what he was looking for. "No" he says, "but I found something I thought I'd lost - faith to keep looking."