Season 2: End Game (2X17)

Writer: Frank Spotnitz
Director: Rob Bowman

Samantha confides in her brother, telling Mulder she was returned to earth some time ago and has been living with 'visitors' to the planet. The doctors who all look alike are really alien clones living on earth, just like her adopted father. But the colony is under threat from an alien bounty hunter sent to kill them.

Meanwhile Scully is taken hostage by the mysterious alien bounty hunter who has the ability to morph himself to look like other people. He demands to know where Mulder is but Scully refuses to co-operate. The alien bounty hunter holds Scully ransom in exchange for Samantha. Mulder sets a trap for him with the help of Assistant Director Skinner, but it goes awry and the alien bounty hunter and Samantha tumble off a bridge in to the water below.

Mulder is devastated at loosing his sister again so suddenly and has to break the news to his parents. Bill Mulder gives Mulder a letter that Samantha left for him should anything happen to her. It contains a key and the address of an abortion clinic. Mulder goes there and encounters more 'Samanthas', it turns out one of them pretended to be his sister Samantha in an attempt to get him to protect them. But they are too late as the alien bounty hunter finds them and kills the last of the clones. Mulder risks his life and tracks the alien bounty hunter in a effort to find out about his sister but ends up being exposed to a toxic alien poison and is left for dead high up in the arctic. Scully tries desperately to find Mulder before it is too late.

Notes:
In order to recreate the Arctic, a large soundstage had to be filled with 140 tons of ice for 5 days.

In the original script, Samantha would have survived the fall off the bridge. Once she had been rescued from the river, she would have driven with Mulder to the clinic. However, once they got there, she would have transformed into the alien bounty hunter.

Apart from setting up the excellent scene with Skinner, why did X show up at Mulder's apartment expecting to see Mulder when he knew he already left to find the ship?
The first takes of the fight between Skinner and X were rather weak as both actors were too preoccupied with not hurting the other. However, after a few takes, the director asked them to heat things up and both decided to just go for it. In the next take, the fight became so real that Mitch Pileggi threw Steven Williams against the (fake) elevator wall so hard that he went right through the back of the set piece.

After Samantha's body is pulled from the river, the body is loaded into an ambulance that carries the letters "FBI." The real FBI doesn't operate any ambulances.

The Bounty Hunter isn't sabotaging anything. It's been well documented on this site and throughout the show that the syndicate's primary mode of covering evidence is immediate termination. The need for the cover-up came when Agent Mulder received information on the alien clones that was likely leaked out by the clones themselves. And what happens when someone betrays the project? They die. The need for the bounty hunter of course was to have an experienced alien assassin.

Although these two episodes hold up pretty well when watched alone, with respect to the larger conspiracy of later seasons, they don't make much sense. If the aliens are cooperating with the Syndicate on Colonization, why would they send a bounty hunter to sabotage the project, especially since the bounty hunter is working with them?

Quotes:
Bounty 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.
Bounty Hunter: She's alive. Can you die now?

X: You wanted to see me?
Mulder: How was the opera?
X: Wonderful. I've never slept better. I don't like these hasty public meetings, Agent Mulder.
Mulder: I'm sorry. I need your help.
X: It's over. The fat lady is singing.

Scully: Did you find what you were looking for?
Mulder: No. No, but I found something I thought I'd lost. Faith to keep looking.

Episode Number: 41
Season Number: 2
First Aired: Friday February 17, 1995
Production Code: 2X17

Season 2: Colony (2X16)

Story by: David Duchovny and Chris Carter
Writer: Chris Carter
Director: Nick Marck

Anonymous email postings draw the attention of Mulder and Scully to the deaths of two identical doctors, killed in arson attacks on abortion clinics up and down the north eastern states. With one outstanding feature, no bodies were recovered from the ashes. Mulder and Scully discover that someone is running newspaper adverts with a picture of the doctor, trying to find other look alikes across the country.

When they manage to track one down, a doctor living in Syracuse, they get a local FBI Agent to protect the doctor until they can get there. But when they arrive agent Weiss tells them that the doctor is gone. On his return to Washington Mulder is called to Assistant Director Skinner's office, agent Weiss has been found dead in Syracuse and Mulder is held accountable.

Taken off the case by Assistant Director Skinner, Mulder and Scully are approached by CIA agent Ambrose Chapel who makes claims that the doctors are Russian clones left over from the Cold War, planted in the US to carry out sabotage in the event of war. That the doctors are being killed off to cover the existence of the Russian's cloning program. Mulder is once again contacted by Assistant Director Skinner, who tells him he has a family emergency. When Mulder arrives home, his father Bill meets him on the porch. As they talk Mulder notices his mother, Teena talking with a young woman, when he asks his father who she is, Bill Mulder tells him that his long lost sister Samantha has been returned.

Notes:
The FBI doesn't have a field office in Syracuse, New York.

The now infamous sound of the alien stiletto is co-producer Paul Rabwin making a 'pfft' sound in the microphone.

Quotes:
Samantha: Is it too late for a game of stratego?
Mulder: It's 22 years too late.

Scully: Well, nothing about it makes sense. We've got three deaths of identical victims, no bodies, a virtual non-suspect...
Mulder: Sounds just like an X-File.

Mulder: I have lived with a fragile faith built on the ether of vague memories from an experience that I can neither prove nor explain.When I was twelve, my sister was taken from me, taken from our home by a force that I came to believe was extraterrestrial. What happened to me out on the ice has justified every belief. If I should die now, it would be with the certainty that my faith has been righteous. And if, through death, larger mysteries are revealed, I will have already learned the answer to the question that has driven me here... that there is intelligent life in the universe other than our own... that they are here among us... and that they have begun to colonize.

Mulder: Who is Mum talking to?
Bill Mulder: Your sister.

Episode Number: 40
Season Number: 2
First Aired: Friday February 10, 1995
Production Code: 2X16