After taking off about 3 weeks from the development tasks for personal reasons and working far too many hours, I have decided that the idea of a mission is going to be scrapped from the game. The problem with missions is that it forces the game down a path that violates some of the ideas I want to create.
For example, the environment the game operates within is entirely procedural. If I create a mission, in order to test a successful outcome, means I must introduce fixed numbers in order for the game to have testable outcomes. This makes the idea of a procedural game static in nature, hampering the ability to be open-ended and random.
Instead missions will be replaced by a goal of setting up a complex on another world with a given set of characteristics. Or setting up a complex on several planets that are N light years apart. This allows the game to still be random, and it allows us to introduce more phenomena in the space between stars.