B.J Morrow is having an affair with her boss, LT. Tillman, and tells him she's pregnant. Inexplicably, she finds herself later in a field, digging up the body of an FBI agent who's been missing since 1942.
Before his disappearance, the agent, Sam Chaney, had been investigating a serial killer who carved the word 'Sister' into the chests of female victims and painted on the wall with their blood. The killer was never caught.
Talking with Scully, B.J admits she's pregnant and having strange nightmares. She doesn't know how she found the body. Scully discovers that the word 'Brother' is carved in the ribs. Tillman tells them there was a recent homicide featuring the same M.O, and another body turns up with 'Sister' carved on it.
Flipping through old mug shots, B.J. picks out Harry Cokely, who was convicted of raping a woman in 1945 and carving 'Sister' on her. Yet when Mulder and Scully visit Cokely, he's feeble-77 year old and on an oxygen machine. When questioned he complains that due to his condition he is unable to leave the house and now just watches TV all day.
B.J. awakens with a vision, soaked with blood, 'Sister' carved on her chest. She says she saw Cokely in her dream and rushes to a house, ripping up floorboards to reveal bones of Chaney's missing partner. It's a house Cokely rented 50 years earlier.
Mulder and Scully visit the women Cokely raped, and she admits to having a baby after the assault that she gave up for adoption. Mulder thinks Cokely's descendant is responsible- the killer's genetic memory having been passed on. The agents discover that B.J. is Cokely's granddaughter.
Mulder fears B.J. will try to finish what Cokely started, and she does go after her grandmother. However she sees 'Sister' carved on the women which fazes her, and instead she hunts down Cokely. Mulder finds him slashed up and is ambushed by B.J., who holds a razor to his throat before dropping the weapon when Cokely dies.
Scully hypothesizes that B.J.'s pregnancy may have been a catalyst for her transformation. She's held in a psychiatric cell on suicide watch, after trying to abort her unborn child, a boy, which Tillman is trying to adopt.