Of of a sudden, the X-Files has a habit of dropping complete bombshells on you and the plot thickens by miles. This is such an episode which basically has the smoking man narrating the entire alien colonization plans to someone.

It all starts with another train car, and some doctors doing an experiment. Some guys from ‘Roush’ again are performing an operation on a person, who seems to be the first successful human\alien hybrid, but before they can celebrate – alien rebels come out from nowhere and burn them all… with the exception of Cassandra Spender – the person being experimented on. Agent Spender and Skinner rush to the train yard where she’s been found, but she only wants to speak to Mulder.

Meanwhile smoking man informs us via narration that the plans for alien colonization which have been in the works for 50 years were going perfectly until the rebels arrived. His own son, who was put in place to protect the project by way of taking over the X-Files doesn’t believe in alien life, and therefore cannot accept the responsibility of knowing the truth. Mulder gets information about Cassandra’s request to chat, and they both head for the hospital.

Amazed that Cassandra no longer needs a wheelchair she tells them that the aliens are there to wipe out human life, and they will do so using the black oil – which she knows as purity. The rebels are here to stop it. She can also identify the men involved, one of which is her ex-husband. Mulder and Scully immediately try to put the pieces together and ‘borrow’ Agent Spenders computer to look up his family, they find that smoking man has a name! “C.G.B Spender” is all they can find. Mulder also sees a picture of Smoking man and his father talking.

Skinner pops in to warn them that they must leave, but it’s too late – Spender finds them and starts the motions of getting them kicked out of the FBI, and Mulder and Scully are put on administration leave. Spender goes to his father, stating he has done all that’s been asked, and in return he wants the truth – Smoking man states that Spender isn’t ready to hear the truth, not accept the responsibility to handle it and gives him a couple of slaps. Spender, eager to prove his worth accepts a job from his dad. We hear Smoking man (yes we know he has a name now but smoking man has stuck!) talking to the rest of the group when one member suggests siding with the alien rebels – this is met with mixed reactions, but it’s Krycek who has the ultimate say, stating that people like Bill Mulder left the group because no one considered it.

Finally, Spender’s been tasked with killing one of the members of the group who’s actually a human\alien hybrid – he’s given the ice pick weapon, and told to stab him in the back of the neck. In true Spender style, he screws it up. Krycek however saves the day and does the job properly.

It’s here when Sender learns that Smoking man directs the project which performed the experiments on his mother. Skinner goes to see Scully and Mulder who claim they’ve figured out Spenders involvement and that Cassandra’s life is in danger. Cassandra escapes to Mulder’s apartment (we don’t know how she found it), and demands Mulder kill her. If she doesn’t die, then there’s no stopping the invasion. Smoking man finishes his narration with a request for help, he’s never trusted anyone except for one person.

She accepts Smoking man’s request for help, and we see Diana leave the room! Mulder draws his gun on Cassandra and asks Scully to step back.

End of part 1.