From their announcement:
I want to answer a couple of questions I’ve been asked many times since the release.
Q: Is this going to be character based or ship based?
A: A Ship to Ship combat game – Pre-painted plastic minis where 2 players play head to head. It will use the HeroClix combat dial to track HPs, attack, damage, etc. Ship figures will not play with Marvel or DC characters though.
Q: Is this going to be a clix game or board game?
A: A co-op euro style strategy game where you will play 1 of the ST crew and work with others to complete missions, just like the movies/TV shows. Again, the HeroClix dial will be used to track stats (skills – in the case of the co-op game).