TWO FATHERS

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. When Dr. Eugene Openshaw arrives, he is informed that their twenty-five-year-old project is finally completed. 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. Walter Skinner takes her son, Jeffrey Spender, to the scene, where he meets with his mother. Cassandra refuses to talk with Jeffrey about what happened to her because she knows that he won't believe her. She asks for Fox Mulder (David Duchovny). Spender then 'asks' Mulder to join him to meet his mother, but Mulder sees it as an attempt to entrap him. 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. The Cigarette Smoking Man's reaction leads to Dr. Openshaw's death. Meanwhile one of the Syndicate elders is killed by an alien rebel, who then takes on his form.

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. Afterwards, Mulder and Scully visit Cassandra at the hospital who informs them that the aliens are here to destroy all life on Earth, further stating that this alien threat moves through the Universe to colonize other planets. She claims that a rebel force of aliens are mutilating their faces to prevent infection by the black oil.

Alex Krycek reports to the Syndicate on the rebel's recent attacks. The rebel, masquerading as the elder he killed, proposes that the Syndicate align themselves with the rebels. The Cigarette Smoking Man seems to recognize that the elder has opposed his own previous opinion—that siding with the rebels is suicide.

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. Spender. Their unauthorized entry at the X-Files office is discovered by Agent Spender, resulting in both agents' immediate suspension from the FBI. Agent Spender, who then reports to the Cigarette Smoking Man demanding the truth. Scully meets with Mulder, telling him that C.G.B. Spender is likely another alias and that the man is linked with Mulder's father, William, who he had worked with on the secret state project. The Cigarette Smoking Man decides to give Agent Spender more responsibility by having him kill the alien rebel masquerading as a Syndicate elder. Spender fails in his task, but Krycek comes to his aid and finishes. Krycek reveals to Spender that his father was responsible for his mother's (Cassandra's) abductions and that his role is to protect his father's stake in the project. This fact upsets Agent Spender.

The Cigarette Smoking Man then reveals everything to Agent Diana Fowley, who agrees to help him. Mulder tells Skinner that Cassandra is in danger because she is the first successful alien-human hybrid; Skinner goes to the hospital to check on Cassandra but finds her gone. 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

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