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So I've been able to figure out which parts to play and when to revisit parts until now, but now I'm stuck in the game with no new stories and seemingly no information to progress further.
Here's what I deem relevant to describe where I'm at: I know Q's origin and his passcode. The last story I was able to play was the AB game, all the way through to where Carlos has decided to find out who Q is, having previously been attacked by the Q with the red eyes.
I haven't come across any information that seemed important or usable for the parts where I have to input something.
Obviously I want to avoid having the game spoiled as much as possible, so I'd really just like to know where I'm supposed to go next and in what story I've missed some important information, if anywhere.
I'm pretty sure the thing with Carlos will open up another path along the right-most path since that's where he ends up. Play that and it should give you an event. Then replay Q team (if you haven't already) on that same path to see the change.