Well... Something I was thinking about was maybe setting it across multiple universes. I mean, maybe starting in the Halo Universe, but then getting thrown into the Star Wars Universe, then maybe showing up in the Doctor Who universe for a little while.

As for story. I was thinking something along the lines of a single villain. Said villain is travelling across the multiverse, stealing technologies and amassing allies in order to create the first Multiversal Empire. Naturally, each of us have a run in with his ship and managing to follow him through the Multiversal travel vortex to the next universe.

Slightly inspired by the Voyager episode Year of Hell. At the same time, I was thinking of maybe some time travel shenanigans. I was thinking of one possible episode involving their combined forces actually managing to defeat the bad-guy's ship, but it escaping back to earth, 2015. It would be interesting for the Battlestar Galactica and Star Wars crews, the former finally getting to visit the fabled cradle of human civilization, and the latter maybe being convinced that Earth is just Corellia from the distant past.

"But I thought Star Wars was a Long Time Ago..."