If it were me, I would base the whole potentially multi-season arc around the whole question of who was responsible for the Moon getting shot off into space and why. I'd do as a arc going on alongside planet/alien of the week stories. Season 1's arc would deal with them trying to figure out why the accident happened and who was responsible for it, with the finale having them get those answers. That would lead into Season 2's arc, where they find out that whoever did it had a specific goal in mind for them, and then any seasons after that would be focused on different aspects of that goal.Though now that you mention it, I like the idea of it just being a mysterious force...aliens, multidimensional "higher" beings (things we can't understand)...maybe just some "force" that is never explain, like the one that destroyed the Moon in Neil Stephenson's Seveneves