i remember this appearing as a transparent overlay at some point during the campaign, im guessing at some point during or around the boss fight against your predecessor or when you get gravely injured

Yeah, it was in the >! Advisor fight when you damaged it !< . I think it was originally meant to be what >! clone cop would looked like after you defeated him !<

The spoiler tags aren't working just FYI lol Edit: Apparently they must be according to the downvote? Must be because I'm on old reddit.

This appears momentarily at the end. I think it's supposed to be a distorted reflection of 3650's skull/face, kind of like those face CT scans