Spoilers for the new movie!
What I don't understand is by the end of Season 9 it was clear Super Soldiers had infiltrated all levels of the FBI and they were no longer safe. Mulder had to hide a whole season and the last time he was at the FBI he got chased terminator style all over..
But now suddenly all is forgiven. Despite being a convicted murderer and being sentenced to death all it takes is one missing FBI agent to basically wipe the slate clean? Also what kind of hiding was it really with Scully openly working under her real name. It just doesn't make sense and it an insult to everyone who followed the show for 9 years (regardless of the quality of the movie). I had really hoped it was like Mulder said a ploy to smoke him out and at the end of the movie they would have to run.. but no. Apparently the Aliens are happy to let a man run around who knows their plans and the government is willing to forgive a murderer..
Also how can Scully/Skinner be so calm about starting a new life when she knows only four years from now colonization will begin!?
The very least they could of done was use false identity's and the movie could pretty much have gone on as it did without making a mockery of all that has gone before it.