Ascension by N.J. Tanger

Synopsis:

The Chimera‘s navigator dies in mysterious circumstances, stranding the colony ship light years from Earth. The AI which makes faster than light travel possible rejects all backup navigators, leaving the ship dead in the water. With social order breaking down and time running out, the Chimera gives Navigator’s Assistant Samuelson a strange, likely impossible task: Find a replacement navigator among the 40,000 colonists and crew. 
 
Something has gone terribly wrong with the Chimera‘s AI, and with the help of his talented girlfriend Amaya, Samuelson plans to find out what. With anarchy and chaos overtaking the ship, and working against the new, self-appointed captain, Samuelson and Amaya discover a dark presence at work behind the scenes, one intimately connected to Samuelson’s past. Only by overcoming his personal demons can he save the Chimera–if he doesn’t lose his sanity in the process.