Sigma Star Saga (2005)

The main character is Ian Recker, a decorated pilot who goes undercover to investigate the enemy species known as Krill. The Krill attacked Earth by gouging out a hole the size of Canada under the Atlantic Ocean, which caused the oceans to boil, nearly destroying all life on Earth. Recker gets "captured" by the Krill, who outfit him with a Krill parasite where he quickly becomes embroiled in a race across several planets for control of mysterious "bio-matter" in the cores of the planets. (wiki)