When I ran some tabletop rpg's I'd start by drawing a network of plots and participants. Who are the powerful NPC's and organizations in the world, what are they up to? I'd usually try to create layered plots, where the players might interact with a henchman of some shadowy figure at the start, and gradually get deeper into the plot as they went. Another useful trick is to have multiple versions of plots: Maybe the planetary governor is stealing money for himself, or siphoning it off to support the rebels, or is actually feeding it into your ultra-secret intelligence service who's keeping that detail from you. By having a couple alternatives, you can choose an outcome based on the rest of the ongoing story (e.g., a strong rebellion has him siphoning it off to support the rebels, a runaway intelligence agency causes the latter case).
In an actively GM'd game that was sufficient, but in your case I'd then create a new network showing major paths through the plots. How could the supernova plot turn out? What plots might feed into it and flow out of it? What are some interesting one-shot events that don't connect a major plot arc? What preconditions make sense for them?
From there, I'd set the preconditions to each event (e.g., rebellion strength >50, science level < 10), outcomes of each choice (rebellion strength + 2, set 'super nova prevented flag' to true), script them up and let the player loose.
