Agent Mulder, unconscious and suffering from severe hypothermia, is transported by helicopter to a base in Alaska. Scully rushes to her partner's aid, and immediately clashes with doctors at the scene. When Mulder's heart stops, she insists he be removed from a tub of warm water because the cold is the only thing keeping him alive. With the doctors locked in a stalemate, the sequence of events leading to Mulder's condition unfolds...
     A research vessel sailing in the Arctic Circle encounters what appears to be a UFO crashing into the Beaufort Sea. But the news media reports that the spacecraft was, in actuality, a Russian plane. The pilot of that craft, a bounty hunter, disappears, and later begins killing doctors at abortion clinics across the United States, setting fires to cover the crime. Mulder discovers that the doctors, though unrelated by birth, look identical. The mystery deepens when it is discovered that officials never recovered bodies from the burned clinics.
     The agents uncover evidence that the killer ran ads in local newspapers in an effort to locate his targets. They realize his next intended victim is a doctor in Syracuse. Mulder notifies Agent Weiss to guard the doctor until they arrived at the scene. But Weiss discovers the bounty hunter standing over the doctor's corpse (which Is slowly dissolving-as if dipped in acid). Weiss opens fire on the bounty hunter, but his bullets prove ineffective. When Mulder and Scully arrive in Syracuse, Weiss tells them there was no sign of the doctor. Unknown to the agents, the bounty hunter is capable of morphing into different shapes, allowing him to assume Weiss' identity. When Mulder return to Washington to meet with Skinner, he learns that Weiss has been killed.
     A CIA agent named Ambrose Chapel approaches Mulder and Scully. He claims that during the Cold war Soviet scientists discovered how to clone DNA. They planted clones in strategic positions within America's medical establishment, hoping to sabotage the country's immune system in the event of war. Chapel believes a secret agreement exists that sent the bounty hunter to eliminate the clones in exchange for absolute suppression of the program's existence. The clones, Chapel suspects, were attempting to contact the agents, hoping they would expose the plot.
     Mulder flies home when he receives word there was a family emergency-losing contact with Scully in the process. When he arrives, he is shocked to discover his sister Samantha-who had been abducted by a UFO as a child-in the company of his parents.
     Samantha tells Mulder that after her abduction she was placed in the care of visitors from another planet, and then made to forget her real family. She used hypnotic therapy to uncover her buried memories and locate her family. She asks Mulder to help stop the bounty hunter before he kills her adoptive father.
     Scully discovers more of the clones hiding in an industrial building. She has them placed in maximum protective custody. Mulder finally locates Scully and enters her hotel room. But Scully realizes the man standing in her room is not the real Mulder...