Books like Zero Hour

United Nations Special Operations Command sent an elite Expeditionary Force of soldiers and pilots out on a simple recon mission, and somehow along the way they sparked an alien civil war. Now the not-at-all-Merry Band of Pirates is in desperate trouble, again. Their stolen alien starship is falling apart, thousands of lightyears from home. The ancient alien AI they nicknamed ‘Skippy’ is apparently dead, and even if they can by some miracle revive him, he might never be the same.