Honestly, I had little success in pure free-roam RPs as they are a pain to manage and have everyone engaged. Nor this will be a good guys vs. bad guys scenario because right and wrong will all be quite relative. The characters will belong to a group, but how they will steer it and what choices they make will impact it's development. For example, it's up to the characters to decide how to deal with a lunatic who went on a rampage after his awakening. And just as it happens, you could use this opportunity to test certain alien tech on that person which WILL turn him into a rampaging monstrosity, just so you can observe the effects up close and try to figure out how to reverse (engineer) the process.