Revelation space Alastair Reynolds.

Dr. Dan Sylveste, an archaeologist who has for years been fascinated with the long-dead alien race the Amarantin, is about to discover something that could change the course of mankind. But before he can act on anything his wife is killed and he is captured when a coup sweeps across the planet Resurgam. Meanwhile, an astonishing ship bearing a crew of militaristic cyborgs and a kidnapped Gunnery Officer is bearing down on Resurgam, crossing light years of space to enlist Sylveste's help to save their metamorphosing Captain. Only Sylveste, or, more accurately, the software programmed containing his father's knowledge that he carries in his mind, can save the Captain. None of them can anticipate the cataclysm that will result when they meet, a cataclysm that will sweep through space and could determine the ultimate fate of humanity.