Deep beneath the frigid waters of the Beaufort Sea in the Arctic Circle, crewmen aboard a submarine investigate sonar readings that indicate a huge, unidentified craft is floating nearby. The submarine's captain receives orders to destroy the vessel without further investigation. Before torpedoes are launched, however, a powerful shock wave disables the submarine's reactors.
     Meanwhile, a bewildered Scully receives a telephone call from Mulder as, simultaneously, a man who appears to be Mulder (the alien bounty hunter from the previous episode) shows up at her motel room. The doppelganger overpowers Scully, and demands to know where he can find Mulder. When Scully refuses to cooperate, the doppelganger throws her across the room.
     The real Mulder and his sister, Samantha, arrive at the motel some time later. Scully is gone, but signs of a struggle are evident. Samantha tells Mulder that the bounty hunter is interested in her, not Scully. Samantha explains that the only way the bounty hunter can be killed is to pierce the base of his skull. She warns, however, that his blood is toxic, and exposure to humans is fatal.
     Samantha assures her brother that the bounty hunter will contact them. As they await word, Samantha explains that aliens have been attempting to establish a colony on Earth since the late 1940s. But their experiments with cloning was not sanctioned, and others of their race considered it a dilution of the species. A bounty hunter was dispatched to terminate the colony.
     Scully, held at gun point, telephones Mulder and arranges a rendezvous at a bridge. Mulder informs Skinner of the situation, and an FBI sharpshooter is positioned nearby. The exchange is made, and the bounty hunter walks Samantha toward an awaiting van. Suddenly, the sharpshooter's bullet rings out. The bounty hunter is struck in the neck. He falls backwards over the bridge, still clinging to Samantha. The pair plummet into the dark, icy waters below.
     Mulder relays news of his sister's apparent death to his father. Mr. Mulder gives his son an envelope, which Samantha had left behind during her visit. Mulder opens it and finds a key and address inside. Mulder travels to the address, which turns out to be an abortion clinic. Inside, Mulder is shocked to discover alien clones who look like his sister. Suddenly, the bounty hunter appears and knocks Mulder unconscious. A fire races through the building, but Mulder is saved by firefighters.
     X tells Mulder that all the clones, save the original "Samantha," was killed in the fire. He also admits that the bounty hunter is inside a vessel beneath the Beaufort Sea. Meanwhile, pathologists tell Scully that a strange retrovirus found in Agent Weiss's blood is inhibited by extreme cold. This leads Scully to conclude that the bounty hunter may have survived his fall into the icy river.
     Mulder makes the trip to Alaska by himself in secret. He finds the submarine's conning tower protruding from the ice. Inside, he encounters the bounty hunter. During a stuggle, the bounty hunter bleeds green ooze onto Mulder. Mulder is pushed outside the sub, and shortly thereafter the vessel descends beneath the ice. Mulder's body is rushed to a military field hospital. Scully arrives at the scene. She realizes that Mulder has been infected with the alien retrovirus. She convinces physicians to lower Mulder's body temperature to counteract the virus. Her efforts are successful, and Mulder's life is saved.