An alien rebellion leads the Syndicate to its demise as their twenty-five year conspiracy approaches its disastrous collapse.
"One Son" begins as Cassandra Spender demands that agent Fox Mulder kill her. Before Mulder can do anything, the front door is smashed open by a group of people in anti-contaminant suits, including Diana Fowley. The intruders capture Dana Scully, Mulder, and Cassandra and bring them to a Centers for Disease Control facility at Fort Marlene. Fowley tells Mulder and Scully that agent Jeffrey Spender called her in because Cassandra Spender has contracted a contagious organism of unknown origin. Scully gets upset at Diana, but Mulder believes her explanation. Meanwhile, Alex Krycek reports on Cassandra's escape to the Syndicate, saying that the alien rebels want Cassandra kept alive. Regardless, the Syndicate decides to turn Cassandra over to the colonists and start colonization in order to save themselves.At Fort Marlene, Mulder runs into the sickly looking Marita Covarrubias. Marita tells Mulder she was subject to experiments by the Syndicate to create a black oil vaccine and the colonists will begin colonization if they learn of Cassandra's existence as an alien-human hybrid. Scully, with help from the Lone Gunmen, looks into Diana Fowley's personal history and informs Mulder that Fowley has been collecting data on alien abductees and heading to Tunisia every week, although there is no trace of her activities in FBI records. Mulder still trusts Diana but goes to her apartment to see her, finding the Cigarette Smoking Man there instead. Held at gunpoint, CSM tells Mulder that he has been betrayed by his son Jeffrey.
CSM tells Mulder the Syndicate agreed by majority vote, against Bill Mulder's objections, to align with the alien colonists in order to delay colonization. The colonists forced the Syndicate to give up members of their own families in exchange for the alien fetus (seen in "The Erlenmeyer Flask"). Because Bill Mulder was slow to cooperate, Samantha Mulder was taken later than the others. Using the fetus, the Syndicate worked on creating alien-human hybrids who could survive colonization. The Cigarette Smoking Man tells Mulder that colonization will begin once Cassandra is handed over and that Mulder will be able to see his sister again, providing him with an address to the hangar where the Syndicate members will be meeting the colonists.
Jeffrey goes to Syndicate headquarters, finding only Krycek there. Krycek tells him that the Syndicate members are preparing to be given the hybrid genes—except for Spender's father, who has gone to retrieve Cassandra. Diana returns to her apartment, finding Mulder there, and the two head to the hangar at El Rico Air Force Base. Jeffrey arrives at the hospital, finding his mother gone. However, while at the hospital he finds Marita, who tells him how to get to El Rico Air Force Base. A Syndicate surgeon attempting to procure the alien fetus is killed by one of the alien rebels, who takes his form. Mulder contacts Scully and the two try but fail to stop the train transporting Cassandra to El Rico. Krycek finds the dead surgeon and the fetus missing and tells Jeffrey the rebels are going to win.
The Syndicate and their families gather at El Rico Air Force Base. Shortly after the CSM and Diana Fowley arrive, a white light appears around the base. It is revealed to be the rebels, who kill the entire Syndicate while CSM and Diana Fowley escape. The next day Mulder, Scully, Walter Skinner, and Jeffrey report to Assistant Director Alvin Kersh on the deaths of the Syndicate. Jeffrey tells Kersh that Mulder and Scully could have prevented it. He resigns and recommends that they be reassigned to the X-Files. Heading to the X-Files office in the basement, Jeffrey finds CSM, who then shoots Jeffrey and leaves.
- The alien colonists in this episode were played by young girls in costumes, as Steven Spielberg's Close Encounters of the Third Kind aliens also were, Spielberg seeing girls as more delicate and graceful than young boys.
- Although the train carrying the Cigarette Smoking Man and Cassandra Spender near the conclusion of this episode appears to be travelling at high speed, in reality it never got above eight miles an hour, the speed limit in the rail yard used for filming. The illusion was created with sound effects, music, clever camera angles and quick cutting.
- Jo Black-Jacob, who played the murderous nurse, was casting director Rick Millikan's high school drama teacher.
- This episode, which finally puts to rest everything about the government conspiracy with an alien species, begins with a montage of flashbacks stretching back to "The Erlenmeyer Flask".
- This episode marks the final appearance of Cassandra Spender, as well as the First Elder, the Second Elder, the Third Elder, and essentially the rest of the Syndicate.
- William B. Davis as Cigarette Smoking Man
- Chris Owens as Jeffrey Spender
- Nicholas Lea as Alex Krycek
- Mitch Pileggi as Assistant Director Walter Skinner
Special Guest Starring
- Veronica Cartwright as Cassandra Spender
- Laurie Holden as Marita Covarrubias
- Tom Braidwood as Melvin Frohike
- Dean Haglund as Richard Langly
- Bruce Harwood as John Fitzgerald Byers
- Don S. Williams as First Elder
- Al Ruscio as Fourth Elder
- Frank Ertl as Fifth Elder
- James Pickens, Jr. as Assistant Director Alvin Kersh
- Robert Lipton as Head Surgeon
- Peter Donat as William Mulder