I'd probably use freeform events based on narration, no dice included. I'd Draw a map of the ship, establish rooms - how traversable they are, things that the pcs can do to prolong their life, define solutions that could solve the issues and showcase that brute force is not the solution (perhaps by showcasing the demise of a weapons officer on the ship prior to the surveillance system going offline). I would need to know the layout, the time that the aliens require to breach the next room, and loosely the objects that are available to the pcs.