The show centers on FBI special agents Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) who work on cases linked to the paranormal, called X-Files.
In a train car, doctors in chemical suits are making incisions on an unseen patient's stomach; green fluid seeps out of the wounds, which heal themselves.
Moments later, rebel aliens begin to appear and start burning all the doctors, the survivor being Dr. Openshaw and a patient, Cassandra Spender, who had been missing for over a year.
Later on, Dr. Openshaw informs the Cigarette Smoking Man (William B. Davis) about the completion of the project, saying he needs to kill his former wife since she is the first successful alien-human hybrid.
Mulder and partner Dana Scully (Gillian Anderson) go over the crime scene photos from the train car incident and immediately recognize similarities to murders from a year earlier.
Mulder and Scully use the computer on the X-Files' office to find the Cigarette Smoking Man's real identity, that he is Agent Spender's father, C.G.B.
The Cigarette Smoking Man decides to give Agent Spender more responsibility by having him kill the alien rebel masquerading as a Syndicate elder.
Cassandra, having escaped from the hospital, arrives at Mulder's apartment and demands that he shoot her because she is the embodiment of fifty years of work by the Syndicate — an alien-human hybrid that will trigger colonization if the aliens learn of her existence.
"[3] The original script featured various flashback sequences, with actors Peter Donat, William B. Davis and Veronica Cartwright all appearing around twenty-to-thirty years younger.
However, the writers eventually came to the conclusion that it "just didn't [...] work", so they cut out most of that storyline, which ultimately led to the creation of a whole new direction in which the Cigarette Smoking Man provided a monologue explaining the history of the project instead.
Those members of The X-Files crew who had moved with the show from Vancouver to Los Angeles still had problems adjusting to the changes when filming an episode.
Manners stated that he was "very nervous" when filming this scene because the crew needed to create a fire inside the house, which was done by Kelly Kerby and Bobby Calvert.
When the faceless alien attacks the Second Elder, a special effects crew member can be seen behind a window "running with his rig", according to Manners.
[14] However, she was critical of its plot, noting that "the series pretty much just picks Cassandra to be the answer to a lot of questions" concerning the show's mythology.
"[15] However, she criticized the episode's plot, noting that "Two Fathers" was "heading straight down a path already trodden by dozens of books, short stories, movies, and other television shows.