The Last Flight of the Phoenix — Matthew O. Duncan

The war was over except for the crew of the T.S.S. Phoenix. Lost deep in enemy space, crippled, but not dead. The odds of survival were stacked against them, but they were still determined to fight their way back towards allied space.
On New Terra, Roy O'Hara had discovered peace for his spirit and joy in a simple life. Yet he had only fulfilled a portion of the Commander's Prophecy. It told of a darkness that would fall on his new home from the stars and he would be called upon once again to save them all.
The Alliance turned a blind eye to the sudden growth of the Sa'larie Empire just beyond their borders, but some in the intelligent community could see the clues of a new threat. A covert team is sent to discover the truth of the alien's goals and they discover much more than they could have ever imagined.
Different paths of unlikely allies and new foes will intersect in the skies and on the ground of New Terra once again, where everything will change and destinies will collide.