It could be that they were on a plane and wake up on the spaceship and not everything is activated. After exploring the ship it starts to turn on bit by bit and they start figuring out how to fly it.
There are also smaller "military" craft that can be flown and these where used to protect themselves from an alien attack of unknown origin. At some stage they come close to the Earth (I think through a wormhole or something) but have to turn back as they were being attacked again.
I think they eventually get home (through the Bermuda Triangle) but their bodies have been replaced (as if they were never gone).
I read that book in the 80's.