A U.S. submarine in the Arctic gets a reading on what may be a craft, and is ordered to destroy it. Instead, the electronics on the sub are all shorted out, forcing the vessel to use battery power.
Scully tries to apprehend faux Mulder and instead is kidnapped, again. Samantha tells Mulder that the Alien Bounty Hunter will call offering to trade Scully for her. She also says the aliens are vulnerable to stabs to the back of the neck, though their blood is toxic to humans. Also, that the alien clones have been trying to establish a colony on Earth since the 1940s, have worked in abortion clinics for access to fetal tissue to create hybrids, and are being exterminated because the experiments weren't sanctioned and are seen as polluting the alien race.
Skinner agrees to help Mulder in the trade by setting up a sharpshooter to neck-snipe the Bounty Hunter. The plan goes awry when both the Bounty Hunter and Samantha fall off the bridge the trade takes place on. Samantha's body is discovered and found to be alien; not long after, Mulder finds that "Samantha" was one of a set of alien clones working on a biological project. They say they know where the real Samantha is, but are killed soon after by the Bounty Hunter.
Mr. X tells Mulder about the disabled submarine, which came across the Bounty Hunter's ship, as well as an attack fleet sent to destroy the spacecraft; Mulder takes off for the Arctic. Mr. X refuses to give Mulder's location to Scully, but Skinner manages to get the information and tell Scully. In the Arctic, Mulder finds that the sub has surfaced through the ice and only one crew member is still alive. Mulder deduces that he is actually the Bounty Hunter and demands to know where Samantha is; the Bounty Hunter only tells him that Samantha is still alive.
Mulder is exposed to the alien blood when he tries to kill the Bounty Hunter, who takes the sub and leaves Mulder on the ice. Back in the scene that opened the two-parter, Scully manages to convince the doctors that the cold inhibits the retrovirus from the alien blood, and Mulder makes a gradual recovery. Scully admits that the various unknowns in the case suggest the paranormal, but that ultimately her belief in scientific rationales has been strengthened.
Episode Body Count
"Samantha Mulder": dies after falling off the bridge with the Alien Bounty Hunter; her body then dissolves, thus revealing that she is an alien.
Four Samantha clones: killed by the Bounty Hunter.
Submarine crew: the Bounty Hunter kills the entire crew of the USS Allegiance by asphyxiation or execution, but no numbers are given. In the various scenes, it looks to have at least 20 people on it; the actual numbers may be much higher, but cannot be confirmed.
Humans: 20
Creatures: 0
Aliens: 5
Cumulative Body Count (41/202 episodes, 0/2 movies)
Humans: 301
Creatures: 18
Aliens: 23
Grand Total: 342
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