I feel like it could go something like the Elder Scrolls games. Your character enters the world for reasons that are largely irrelevant to the greater story, and while your path ever circles around and toward Carmen's, it doesn't come to a head until the climax of the main storyline. You could choose to be ACME or VILE, and that would affect your interactions with NPCs and any side quests specific to your faction. The educational aspect could come into play, but you'd also solve puzzles and experience combat.))