Introduction
A quick recap on the last episodes of the X-files as a premise to this story:
Mulder and Scully are on the run from the law after Doggett and Skinner helped Mulder escape from military prison
Mulder and Scully's son William was put up for adoption.
William showed signs of supernatural abilities --- telekinesis in particular. And there was a lot of commotion about his birth because as Alex Krycek has said, he was "special" and that he was "perfect". This author assumes that William is the perfect alien human hybrid who will survive the alien invasion.
Before he was put up for adoption, Jeffrey Spender had injected him with a form of metal that may have hampered his abilities and made him more human. However, it was not enough to make him safe from the colonizers.
The colonizers would not approve of people like William because they may be the key to either preventing or stopping the alien invasion.
The alien invasion will probably be a form of genocide, where a virus will infect all human kind --- through virus-carrying bees or the black oil, I'm not sure --- turning them into hosts of an alien life form (as seen in the X-files Feature Film). and the date set for the invasions was December 12, 2012, ten years after the end of the X-files series (2002)
Cigarette Smoking Man and Alex Krycek are assumed to be dead, so there are no possible personalities (that we know of) who are still conspiring with the alien race.
ADs Skinner and Kersh, John Doggett and Monica Reyes are assumed to have been kicked out of the FBI after helping Mulder and Scully escape.
P.S. My apologies to my CSI:NY readers if I'm moving towards another genre. I've just been frustrated with how the Danny-Lindsay dynamic has been thrown in the backburner that I've gravitated back towards my X-files roots.
Anyway, hope you still read this one. Thanks.