So it all boils down to this: Cassandra was left alive by the alien rebels so that the aliens could discover her. Once they would have discovered her, the project would have been exposed. Confused? Me to.
She would have also been made public, and the men behind the project would be exposed to. Smoking man suggests to the group that they turn her over to the aliens, allow them to still save themselves. He’s reminded that Bill Mulder was against this, and that it would be there undoing. Smoking man reminds them that Bill sacrificed Samantha for the project, and that they would like to see their loved ones again that they’ve all sacrificed. The only way to do this is stick with the plan, and let the aliens know what’s been going on.
As for Mulder, Scully and Cassandra – before anything happens, the CDC burst in and take them away – under Diana’s direction. Scully instantly cottons on that it was just an elaborate scheme to get Cassandra away. Now a lot of explanations happen very quickly as it looks like this is the war in it’s entirety. While looking around the CDC, Mulder meets Martia – the woman who has been abducted many times in Scully’s little ‘women’s’ circle.
She tells Mulder she’s been infected with the black oil to work on a cure, and that Cassandra is the real deal – she’s the hybrid. The hybrid project was in corporation with the aliens, but the security council secretly kept the vaccine hidden, and that if the aliens learn of Cassandra, colonization of the planet will begin.
Scully goes to the Lone Gunmen to dig up more dirt on Diana, which raises some questions about her past. There’s a massive gap, and she’s been collecting data on all the women who have been abducted. Mulder blindly follows fate that Diana is on the side of good, but Scully doesn’t seem to think so. With suspicions in mind, Mulder goes to her apartment to find evidence, but only finds Smoking man.
Smoking man, who was looking for his son who betrayed him (believing in Mulder’s cause), goes on to explain what happened years ago. He calls Bill Mulder the lone descender, and goes on to explain how wrong Mulder has been regarding Samantha, his father, and the alien corporation. Bill had objections about making an alliance with the aliens. Smoking man believed it was the right thing to do simply because they stalled the alien invasion, and that they saved billions of lives.
Bill on the other hand knew they hadn’t saved anyone but themselves, working on the vaccine not for the planet, but personally for them. However, there’s a side Bill Mulder failed to realise – it was to ensure Mulder junior’s survival too.
In exchange, each member of the group gave their children away – to become hybrids so they could be seen again in the future by their loved ones. In exchange, the aliens gave them an alien foetus – all they needed to begin working on their own hybrid experiments, and a new race. Bill was slow to come around – hence why Samantha was abducted slightly later. The vaccine however was Bill’s idea, to save everyone.
Things get pretty glum when the security council move out of the building they’ve been in for 50 years, and Cassandra is taken away once again by her ex-husband, to be given to the aliens. Marita is there to hear the information though. Mulder questions Diana, but finds nothing. Only the acceptance of the colonization. He calls his own cause ‘futile’, and he needs to accept that the only way the people he loves will survive, is to give up. Smoking man gave him the location of where they will be meeting to survive the invasion.
Diana gives Mulder a quick snog. Meanwhile, the rebel aliens steal the alien foetus, Scully and Mulder attempt to stop the train carrying Cassandra to the air base, and instead of being saved – the group and their loved ones are surrounded by rebel aliens… and are burnt. Only Smoking man and Diana make it out. Finally, Kersh is trying to make sense of this, Spender takes responsibility for the deaths of the burnt people, and states that Mulder and Scully can explain.. and prevent this from getting worse.
He claims suspending the agents was a mistake and that Kersh should do everything he can to get them back on the X-Files. Spender ignores Kersh, and leaves to pack up his office. Only now does Kersh ask Mulder for answers, who claims he’s had them for years and no ones been listening. Spender is met by Smoking man in Mulder’s old office, in a last attempt to bring loyalty and trust between himself and his son, Spender states he hates him.
To which Smoking man replies ‘Hoping that my son, might live to honour me, like Bill Mulder’s son’. He then shoots Spender.