Dr. Lev (last seen in 8X08) is working late at night in the Zeus Genetics lab, clutching an alien baby when Billy Miles (last seen in 8X15) enters. “Your work here is done,” Billy says. He beheads the doctor with his hand and sets fire to the body. The next day, Doggett is home when Mulder pays him a surprise visit. He shows Doggett a news report on television of a fire at Zeus Genetics. Mulder believes that somebody is covering up whatever was going on in that lab, and Doggett sends Agent Crane to sift through the ashes at the crime scene. The only person not accounted for is Dr. Lev, a partner in Zeus with Dr. Parenti, Scully’s former obstetrician. Mulder and Doggett break into Parenti’s office and are surprised to see the doctor there. When Doggett finds racks of specimen jars with abnormal fetuses, Mulder accuses the doctor of experimenting with alien embryos.
Lizzy Gill leaves Scully’s apartment and is picked up by Duffy Haskell, who was last seen in 8X08 as part of the conspiracy surrounding implanting alien fetuses into abducted women. “I think she trusts me,” Lizzy tells him. In his office, Dr. Parenti packs up the specimen jars when he hears someone come in. It is Billy Miles. Parenti tells him that the office is closed. “Yes, it is,” Billy says calmly. Mulder and Doggett sneak into Parenti’s office in the middle of the night, suspecting foul play when the doctor does not answer their calls. Amid the fetuses, Doggett finds the head of Dr. Parenti in a specimen jar. Suddenly, Billy Miles surprises Mulder and throws him through a glass window. Doggett, seeing the alien vertebrae on Billy, shoots at him but Billy escapes. Later, Scully tends to Mulder’s injured head at her apartment. He tries to explain that Billy has transformed into an alien, but that he himself was somehow prevented from this through Scully’s procedure in the hospital. Yet Billy is no ordinary alien, because Doggett saw red blood when he shot at him. Mulder determines that Billy is now a hybrid, and fears for the safety of Scully’s baby. Lizzy, overhearing their conversation, phones Duffy. Duffy, however, is face-to-face with Billy Miles, and the alien slices off Duffy’s head with one clean chop of his hand.
Duffy’s body is found in an illegal medical facility used for cloning. There, Skinner locates prenatal records on Scully, as monitored by Dr. Lev and Dr. Parenti. Skinner takes Mulder aside and asks about the nature of Scully’s conception, but Mulder, surprisingly, doesn’t have any answers. Mulder calls Scully and says it is important that he immediately see her regarding interference with her pregnancy. Yet she hears a noise in her apartment and catches Lizzy tampering with her prescription bottle. “Who are you?” she demands. Later, after a checkup, the doctor assures Scully that the pills she had been taking were only harmless vitamin supplements. Doggett interrogates Lizzy, who recounts how she worked as a research scientist on human cloning. Her research team had been successful at birthing an alien egg in a human mother. Mulder is outraged. “What did you do to Scully?” he screams. Lizzy tells them that there is nothing wrong with Scully’s child. In fact, it is perfectly human, and she had tried to protect it. Agent Crane informs Doggett that Billy Miles phoned in and offered to give himself up.
A SWAT team storms Dr. Parenti’s office, but Billy is not there. Sensing danger, Mulder orders Scully to quickly pack and leave her apartment. Doggett calls with news of Billy’s disappearance, and mysteriously, the lights go off in Scully’s apartment. Billy misses Mulder and Scully as they escape outside. Their car, however, is blocked in, and the approaching Billy Miles traps them like sitting ducks. Suddenly, another car screeches from out of nowhere and plows over Billy. Mulder and Scully watch in shock as its driver — Krycek — orders them to get in. Billy Miles gets up, unhurt, and watches the car speed off. At the FBI, Krycek informs the assembled agents that the aliens are afraid of Scully’s child because it is greater than they are. Doggett is suspicious of Krycek and calls Agent Monica Reyes, who has flown into Washington, for help. Skinner and Mulder take Scully into the elevator, but as they approach the garage, Doggett calls to say that Billy Miles is down there. They put Scully back in the elevator, and Billy goes up the stairs. Krycek takes Scully while Skinner and Mulder proceed in the elevator, with Billy in pursuit. Doggett puts Scully in a car with Reyes. On the roof, Billy is about to strike Skinner when Mulder comes up from behind to push Billy off the roof. He lands in a garbage truck and its compactor crushes him. As Scully and Reyes speed out of the garage, Agent Crane blocks their path. He watches as the garbage truck rids of Billy, and then waves the women safely by. They do not see that Agent Crane too has the alien vertebrae on his neck.
Original Air Date: 05/13/01
Written by Chris Carter
Directed by Kim Manners
DAVID DUCHOVNY as Special Agent Fox Mulder
GILLIAN ANDERSON as Special Agent Dana Scully
ROBERT PATRICK as Special Agent John Doggett
Nicholas Lea as Alex Krycek
Mitch Pileggi as A.D. Walter Skinner
Annabeth Gish as Special Agent Monica Reyes
Frances Fisher as Lizzy Gill
Jay Acovone as Duffy Haskell
Kirk B.R. Woller as Agent Gene Crane
Sheila Larken as Mrs. Scully
Zachary Ansley as Billy Miles
Steven Anderson as Dr. Parenti
David Purdham as Dr. Lev
Denise Crosby as Dr. Speake
Arlene Pileggi as 1st Woman Party-Goer
Karon Kearney as 2nd Woman Party-Goer