Star Trek: New Frontier, book 05 : Martyr
Peter David1998

With the fall of the ancient Thallonian Empire, civil war threatens the planet of Zondar. The arrival of the U.S.S Excalibur is greeted with relief and celebration by the anxious populace, and Captain Mackenzie Calhoun, fresh from his cataclysmic escape form the Thallonian throneworld, is acclaimed as their prophesied savior. But one believer's messiah is another's blasphemer -- and a prime candidate for martyrdom.

When Captain Calhoun is captured, Lieutenant Commander Burgoyne must find him before an alien fleet launched a holy war against the Federation!