Roboteer / Alex Lamb.

The starship Ariel is on a mission of the utmost secrecy, upon which the fate of thousands of lives depend. Though the ship is a mile long, its six crew are crammed into a space barely large enough for them to stand. Five are officers, geniuses in their field. The other is Will Kuno-Monet, the man responsible for single-handedly running a ship comprised of the most dangerous and delicate technology that mankind has ever devised. He is the Roboteer. Roboteer is a hard-SF novel set in a future in which the colonization of the stars has turned out to be anything but easy, and civilization on Earth has collapsed under the pressure of relentless mutual terrorism. Small human settlements cling to barely habitable planets. Without support from a home-world they have had to develop ways of life heavily dependent on robotics and genetic engineering. Then out of the ruins of Earth's once great empire, a new force arises - a world-spanning religion bent on the conversion of all mankind to its creed. It sends fleets of starships to reclaim the colonies. But the colonies don't want to be reclaimed. Mankind's first interstellar war begins. It is dirty, dangerous and hideously costly. Will is a man bred to interface with the robots that his home-world Galatea desperately needs to survive. He finds himself sent behind enemy lines to discover the secret of their newest weapon. What he discovers will transform their understanding of both science and civilization forever...but at a cost.