Battlestar Galactica: Blood & Chrome.

The first Cylon war has been raging for 10 years and a young Ensign William Adama joins the fleet. He's disappointed not to be assigned to a fighter but to a freighter. His co-pilot, Lt. Coker Fasjovic, isn't too keen on having a rookie flying his aircraft as he has only a short time before he again becomes a civilian. Their cargo is a civilian scientist, Dr. Becca Kelly, but they no sooner leave than she has new orders for them and a new destination. She is less than forthcoming about just what her secret mission is but Adama is keen, particularly as it involves going into Cylon controlled space. Nothing is as it seems however.