Lost Planet (Starship of the Ancients Book 2)

"Evan and Anya have escaped Aethos, but there's no evading the new target on their backs. Everyone wants the ancient alien starship now under Evan's command, and they'll claim it at any cost. Unfortunately, the ship's sentient AI is missing thousands of years of history and is just as surprised to be wanted and on the run. As they embark on an ambitious investigation to track down the ship's markers, Evan and Anya soon discover that the interstellar plot to transform the Commonwealth with alien tech runs deepeer than they'd ever imagined." --