Mission SA3, the final Advanced Simulator mission, seems to be another that hasn't been entirely planned out yet. There is one interesting part, though - plans for including an Easter egg: "We should put in an Easter egg that will allow the player to have weapons, and when he shoots YessMan, he’ll get some sort of prize or cool visual effect… maybe the “secret credits”."
These updates are thanks to John "Captain Johnny" Guentzel, who provided several CD image archives of material used by the Wing Commander Prophecy development team!
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Date: May 2, 1997