Its always been about that. And its tiresome. The real government conspiracies are both more mundane and worse than the science fictional ones from the X-Files that it was supposed to be analogizing. There is no overarching grand plot or some Illuninati,. All of the self-serving bureaucrats and government employees sustain, grow, and protect it are just a bureaucracy that has become an meta-organism.
The show doesn't even make a good release from that reality, since the characters are/were agents of that very same bureaucracy.
I know, I know . . . move along . . . nothing to see here . . . . pay no attention to the man behind the curtain . . . . .
OK James, you got the message out, now go back to the Mothership and report all is well . . . . .
@Tony2X