The unexpected return of Cassandra Spender and an attack by alien rebels forces the Syndicate's hand in a move that threatens the survival of their carefully-crafted conspiracy.
At a rail yard in Arlington, Virginia, doctors perform an operation on an individual who bleeds green blood and instantly heals when cut by a laser scalpel. Another doctor, Eugene Openshaw, arrives and is greeted by the team, who tell him that his work is now a success. Openshaw seems stunned by the news and turns down an offer to celebrate with his group. As the doctors leave, they are attacked by faceless alien rebels and are incinerated. Openshaw is the last one to be set upon, and after setting him ablaze, one of the rebels studies the patient, who is revealed to be Cassandra Spender.
Sitting in a dark office, Cigarette-Smoking Man explains how he and his fellow Syndicate members created a conspiracy to hide the truth about aliens and the planned colonization of Earth, as well as how they had an alliance with the aliens that would see them spared. He goes on to hint that the project has fallen apart, and that his son has betrayed him.
In the X files office, Spender is visited by Skinner, who notes that a status report that Spender is writing is probably the only one he has made since taking up his position, and bluntly speculating that Spender's objective is not to make progress on the X files. Skinner goes on to tell Spender that his mother Cassandra has been found in Virginia, and that she is the only survivor of an arson attack.
They immediately travel out to the site, and Spender finds Cassandra unharmed but dazed. She barely recognizes him, but when she does, she asks for Mulder, infuriating Spender. As he leaves, Skinner follows and recommends that if Spender wants to find the people who abducted Cassandra, he should use every resource at hand, including Mulder.
Scully visits Mulder while he plays basketball at a D.C. gym, and they joke about Mulder's frustrating work load on basic duties at the FBI. Scully informs him that Spender wants to see him.
Mulder finds Spender at Mulder's desk and quickly makes clear his frustrations with him. Spender explains that Cassandra has been found and that she is asking to see him. Mulder spurns the request, deducing that he is being tricked into a position of weakness.
Cigarette-Smoking Man visits Openshaw, who is suffering from extreme third degree burns in a hospital. Openshaw reveals the work on Cassandra was a success and the project is complete. CSM reacts in shock. When Openshaw states that soon people will come to question him, CSM switches off his oxygen supply. As Openshaw calmly waits to die, he notes that "nobody should live long enough to see their children, or their work, destroyed".Second Elder is called by CSM, who informs him that Openshaw and the doctors have been killed, and Cassandra found alive at the site of the burnings. Second Elder agrees to fly in for a meeting with the Syndicate, but before he can prepare is visited by a man who appears to be identical to Openshaw. Realizing what the man is, Second Elder instinctively rips off the man's face, revealing him to be a faceless rebel. The rebel overpowers and incinerates him.
At his desk, Mulder examines photos of the corpses from the train yard. He is visited by Scully, who asks what Spender wanted. Mulder tells her about Cassandra, but says he will not go to see her because he feels it will leave him open to attack from his enemies. Scully notices the photos Mulder is examining and notes the similarity of the burnings to those at Ruskin Dam and Skyland Mountain in 1998. She suggests he visit Cassandra in secret since she may hold the truth about the abductions and tests.At the hospital, Scully meets the under-guard Cassandra, who greets her warmly. When Scully suggests they go for some fresh air, Cassandra shocks her by revealing that she can now walk. They go for a walk, and talk out of ear shot of the guard. Cassandra mentions that she was hoping Mulder was with her, and Scully tells her she has a surprise. She leads Cassandra into a storage room where Mulder is hiding, and again she greets him enthusiastically. Cassandra tells Mulder that his "meeting" with Samantha the previous year wasn't her and that Samantha is still being held by the aliens. She goes on to reveal that she has discovered that the Colonists are taking over the universe using the black oil and that they plan to colonize the Earth by the same method while colluding with men of power. When Mulder asks about those who took her, Cassandra reveals that one of them is her ex-husband and Jeffrey's father.In the meeting room in New York City, Krycek briefs the syndicate, informing them that there have been a series of other rebel attacks on their railroad experiments. As they discuss what they should do about the situation, Second Elder suggests forming an alliance with the rebels in an attempt at resistance. Krycek dismisses this, explaining that the option had been spurned by the Syndicate years before, and angrily telling him that they should continue their plans towards creating a vaccine and using the hybrid program as a delaying measure. Krycek is rebuked by CSM for his persistence on the point.
Mulder and Scully break into the X files office in an attempt to find information on Spender's father. They find a file with minimal information on Cigarette-Smoking Man, which apparently shows that his name is C.G.B. Spender. They are interrupted by Skinner, who tells them to gather what they took and leave quickly. As the three leave, they are intercepted by Spender, who has them suspended.
Spender meets his father at the Syndicate room and makes clear his frustration with having to hound Mulder constantly. CSM angrily tells him that he will follow his father's orders, and that Spender would have nothing if it weren't for him and his connections. Sickened by his son's impertinence, CSM spits that Spender "pales to Fox Mulder".
Scully visits Mulder at the gym, having conducted research into C.G.B. Spender. She notes that it is an alias and one of thousands on record. She shows him a photo that she has found of CSM and Bill Mulder.
Spender meets CSM, who apologises for his earlier behavior. He says he is giving Spender a chance to prove himself, instructing him to visit Second Elder and kill him, as he in an imposter who has infiltrated the group. Although baffled, Spender takes a gimlet weapon proffered by CSM and gets into a car driven by Krycek to the house.
He arrives and introduces himself to Second Elder, claiming that he has to speak with him about a decision made by the Syndicate in regards to the Rebels. When inside, Spender pretends to drop a letter, causing Second Elder to stoop down to take it. With the back of his neck exposed, Spender arms the gimlet but is quickly overpowered by Second Elder. As he is throttled, Spender tears off Second Elder's face, revealing his identity. Krycek appears behind the rebel and kills him with a gimlet of his own.Skinner visits Mulder and Scully at Mulder's apartment, and they tell him that Spender is corrupt and is acting in the best interest of CSM rather than the FBI. They use the data records on C.G.B. Spender as proof. When Scully says that Cassandra is now at risk of being taken again, Skinner insists that she is safe and guarded. Mulder notes the guards were assigned by Spender.At the house of Second Elder, Spender looks at the decomposing alien rebel despairingly and is encouraged by Krycek who tells him that the first experience with an extraterrestrial is always the most painful. Krycek goes on to reveal that Cassandra's experiments are being directed by CSM and that under his guidance Spender will become a great man. Stating that he'll become his own great man, Spender storms out.
Continuing his narration, CSM notes that with his son now turning traitor and his colleagues powerless against the rebel threat, he needs a new ally to help him. It is revealed that the person he is speaking with is Diana Fowley, who agrees to help him before walking out.
Skinner goes to find Cassandra at the hospital but finds only an empty room and no guards. He is met by Spender, who demands to know where she is.
Cassandra shows up at Mulder's apartment in hysterics, stating that she "is the one" and that if she is found and recovered by the Syndicate, it will "all start". She begs Mulder to shoot her, and he raises his weapon as somebody begins banging on his door.
- A deleted scene features Krycek sycophantically showing his respect for Cigarette-Smoking Man and also speculating that somebody would have to take over CSM's role once he was dead. CSM rebukes Krycek, making clear that he does not have faith in Krycek and that he has somebody else in mind as his successor.
- Veronica Cartwright, playing Cassandra Spender, received an Emmy nomination for Outstanding Guest Actress in a Drama Series for her work on "Two Fathers / One Son".
- The idea that the Cigarette-Smoking Man would be telling the story was a very last minute addition as production had even wrapped on this episode.
- This two-parter won the Emmy Award for Outstanding Makeup for a Series.
- In this episode Cassandra wants to end her life because her existence as the first alien/human hybrid signals the beginning of alien colonization. In Greek the name Cassandra means "Prophet of Doom".
- Krycek: Resistance was futile then, why would it be any less so now? 'Resistance is Futile' is a trademark saying of the Borg from Star Trek: The Next Generation.
- The location stamp states that the Elder's residence is in Silver Springs, Maryland. This is incorrect. The correct name of the city is Silver Spring.
- When the faceless alien sets the doctor on fire you can see his fire proof gear clearly
- William B. Davis as Cigarette Smoking Man
- Chris Owens as Jeffrey Spender
- Nicholas Lea as Alex Krycek
- Mitch Pileggi as Assistant Director Walter Skinner
- Veronica Cartwright as Cassandra Spender
- Nick Tate as Dr. Eugene Openshaw
- George Murdock as Second Elder
- Don S. Williams as First Elder
- Al Ruscio as Fourth Elder
- Frank Ertl as Fifth Elder
- James Newman as Doctor