The PCs will pick 3 questions. These should ideally be yes/no questions, and can be about the character’s role in the group, or the character’s relationship to other PCs/NPCs, or the nature of Zion, or the Machines, or the Matrix itself. (If a question is resolved: the player gets to answer questions about themselves or about Zion; the owner of a PC gets to answer questions about that relationship, and the GM answers all other questions.)
The GM and the player will establish the “trigger” for when the question gets answered. It will be some combination (through ANDs or ORs) of the following: Mission failure, Mission success, Agent encountered, PC is killed, NPC is killed.
Also, each question will have a progress track of 0s and 1s. (Initially, it is set to 000.) When a question’s trigger goes off, any player can declare the question closed. In that case, the question is resolved if there are more 1s than 0s. (It is definitely left unresolved otherwise.) (The group should keep in mind that some questions just should remain unresolved, and other questions only make sense if they get resolved, or indeed may get resolved through other events anyway. So some flexibility is good.)
So, how does the progress track get modified? Through missions and interludes. After a mission, if there was relevant information or progress, change a 0 to 1; if there was conflict, turn a 1 to a 0. After an interlude, if there was an open discussion or new ideas being discussed, you change a 0 to a 1; if there was pessimism and doubt, change a 1 to a 0. Interludes are usually between missions, though they sometimes can take place during a mission. (One possibility is an agent decides to have an intimidating conversation with you, rather than trying to flatline you.)
The hope is this: there is a mechanical reason to have the in-character interludes and discussions that are vital for the feel of the Matrix. We’re going to keep relatively freeform in the sense that actual answers are determined by the play group, but the mechanics determine when a question could be closed, and whether the group gets any answers at all.
Open questions: is this too complex (both the tracks of triggers and progress)? Should I collapse or separate them? Do players prefer mechanically determined answers? Will the unresolved questions be interestingly frustrating, or simply frustrating?
(I do feel that some questions won’t get resolved and that can be a good way. If I have a question of whether Shard will ever see me as more than a friend, maybe it’s unresolved, and there’s just too much going on in our battle against the Matrix for us to ever get a true answer.)