When authorities receive a telephone tip from someone named Sidney, the FBI and BATF stage a raid at Temple of the Seven Stars, a religious cult in Apison, Tennessee, which Sidney claims is abusing children and has a cache of illegal firearms. When they arrive they find no sign of the cult leader Vernon Ephesian (Michael Massee), and believe he was tipped off that they would arrive. Agent Fox Mulder (David Duchovny) experiences déjà vu and proceeds out of the temple to a neighboring field, followed by his partner Dana Scully (Gillian Anderson). Mulder leads her to a trapdoor in the field and opens it, finding Ephesian inside with his six wives, who are all about to drink a red liquid. Mulder prevents them from drinking the liquid and handcuffs Ephesian, but he feels a strange connection to one of the women, Melissa Riedal-Ephesian (Kristen Cloke), as if he has seen her before.
Assistant director Walter Skinner (Mitch Pileggi) warns the FBI and BATF that Ephesian and his wives will be released in a day unless they can find hard evidence of the weapons or Sidney. Mulder and Scully question Ephesian, and he states that there was no member of the temple named Sidney. They then interview Melissa, who suddenly begins to talk like Sidney and states that the President of the United States is Harry Truman. Scully believes she is exhibiting multiple personality disorder, but Mulder thinks she is recalling a past life. Mulder and Scully take her back to the temple, where she takes on the personality of a Civil War woman, who says that the weapons were hidden in a secret bunker in a field. She also states that Mulder, in a past life, was in the field with her, and she watched him die.
Mulder takes Melissa to regression hypnosis for her to recount her past lives. She implies that she and Mulder have met over their past lives, only in passing. To confirm her events, Mulder has himself hypnotized. He recalls a time when he was a Jewish Polish woman with a son, who has the same soul as his sister Samantha. His father, who was Scully, is dead, and he is prevented from seeing him by a Gestapo officer who is The Smoking Man. His husband is being taken away from him to a Nazi concentration camp; it seems that Melissa's soul is connected to Mulder's. Mulder also recalls the time he died in the field with his sergeant, who is Scully. In their Civil War lives, he is a man named Sullivan Biddle, while Melissa is Sarah Kavanaugh. Scully finds pictures of the two of them in the county's hall of records and gives them to Mulder.
The FBI and BATF plan to make another search of the compound. Ephesian, realizing that he will not survive another siege, passes out poison to the cult members and all but he and Melissa die, Melissa having feigned drinking it. As Mulder rushes into the temple, Ephesian forces Melissa to drink the poison, and when Mulder arrives he finds both of them dead. Mulder caresses Melissa, looking out into the field.