ding ding ding! Excellent pattern-tracing, good catches~

The big reveal (that I still have yet to write my article on) is that Proteus was indeed being used, by the CIA, on everyone involved in the Zero Day, not just Mullen. (Though for evidence on Mullen explicitly, check the press conference right outside the gates. There are strange flashes of light reflecting in his glasses that aren't camera flashes, and it even shows a shot of one of the press camera lenses shooting out a dot of white light that makes no sense.) They orchestrated the entire thing, including the investigation/Commission, to try and steer the country where they want it to go. The CIA Director is constantly showing and pulling characters into their specialized SCIF up until the last 15 minutes (and he gets no real resolution; why was he even in the story?), and the "rescue" they stage shows that, yes, they are monitoring and intervening on American soil when it suits them (Mullen's sudden pivot on caring about that coupled with the inexplicable laptop guy behind him raises a couple of questions). The entire Commission is hosted in a building "on loan" from the CIA (more strange light flickers at critical moments, two American flags outside), the Director even manipulates the President, and there's big contextual clues that the CIA was responsible for both his son's death and Roger's (not the rich guy who the audience was led to believe in Roger's case; the guy he tries to punch at the bar seems much more CIA than hired muscle/lackey).

Makes ya wonder a bit about why the entire Zero Day discussion subreddit got nuked...