“End Game” is episode seventeen of season two of The X-Files.
The episode opens in the Beaufort Sea, 87 miles north of Deadhorse, Alaska, and a U.S. submarine has detected something on sonar hanging below the ice. The sub’s captain contacts the admiral by satphone and is ordered to destroy what has been spotted. Before that can be done, a high-pitched noise fills the submarine and it loses everything but emergency power. The captain orders them to surface, but they are under 32′ of glacial ice. Surfacing is going to be tricky.
At the end of the previous episode, “Colony”, Scully was in her motel room when Mulder arrived. Then Mulder rang her on the phone, giving her one too many Mulders. It picks up with Scully on the phone to the second Mulder, which she claims is a wrong number. Then draws a gun on the first Mulder. This Mulders says he is getting his ID, then slugs Scully across the room and demands to know where he is. He is far stronger than he should be. Mulder demands again to know where he is, then shifts into what is now known to be the alien bounty hunter.
When Mulder arrives at the motel with Samantha, there are signs of a struggle and Samantha says that he’s been here. That Scully is alive, because the bounty hunter took her to get to Samantha. He will contact them for a trade. Samantha says the bounty hunter wants her dead because she knows how to kill him, by piercing the base of the skull. Mulder points out that would kill anyone, but this is apparently the only way to kill the bounty hunter. Samantha is fairly sure it will work. Samantha explains that the alien blood is toxic, and exposure to it is fatal to humans.
Whilst they are waiting for a call at Mulder’s apartment, he wants to know more from Samantha. Why she came back, about her adoptive parents, the man who wants to kill them. She says that the man is seeking the progeny of the original two visitors, clones who started forming a colony in the late 1940s. There are clones in virtually every part of the country. The aliens think that stewardship of the planet is being forsaken and, in time, they will become its natural heirs by default.
The clones have been trying to erase the aspect that forced them to scatter, their identical natures. Working at abortion clinics gave them access to foetal tissue. The clones were attempting to combine human an alien DNA. The experiments were not sanction, and are considered to be a dilution of their species, which is why the bounty hunter has been sent to kill them.
As they are waiting, a knock on the door is AD Skinner. Mulder speaks to him as his sister sneaks behind Skinner. Skinner says that Scully incarcerated four men at the federal marshals’ office, who are now missing – clones, and the bounty hunter found them. Samantha says that Skinner isn’t the bounty hunter. Mulder tells Skinner that Scully is missing, then she calls, telling Mulder what the bounty hunter wants – Samantha in exchange for her. The bounty hunter is not interested in negotiation and Mulder wants Skinner’s help and trust.
At the site of the meeting, Ole Memorial Bridge in Bethesda, Skinner is waiting with a sniper as Mulder and Samantha wait in a car. The bounty hunter arrives with Scully. The sniper has no shot. Scully is exchanged for Samantha, and Samantha tries to kill the bounty hunter, but fails. The sniper manages to get a shot, and both the bounty hunter and Samantha fall off the bridge into the water.
Divers are working the next day but haven’t found anything when Scully shows up. Mulder didn’t tell her who Samantha was, because he knew Scully wouldn’t have let him go through with it. Scully wants to know if Mulder is sure it was Samantha, given her experiences with a shapechanging bounty hunter. Mulder is, and has already told Skinner they were dealing with an alien. That was the easy part. Mulder now has to tell his father. This does not go well. Samantha also left an envelope for Mulder at the house.
The envelope contains a letter and a passcard, which lead to another abortion clinic. Mulder heads there and Scully calls him. He thinks Samantha is still alive; she tells him to return because they have just recovered her body. Mulder will be there shortly but, after he hangs up, Scully is called by one of the paramedics. Samantha’s body is dissolving into green goo. Perhaps she wasn’t Mulder’s sister.
At the clinic, Mulder finds another woman. Samantha. Then more of them. He now has far too many sisters. The women claim they needed his help and knew he could be manipulated using her. There is a man coming to kill them, and they aren’t convinced by Mulder saying that he’s dead. The women want Mulder to save the first of them – because they know where his sister is. Before they get much further, the fire alarm goes off. It seems the bounty hunter isn’t as dead as he could be.
Mulder ends up going off on his own, after meeting with Mr. X. Scully’s investigations reveal why she was so insistent at the start of the previous episode that Mulder be kept cold. Skinner is becoming more of an ally as well, taking some matters into his own hands.