The Faraian Conspiracy by Kai Starr

Agent Jason Ebert (aka Genjiro Nakadai) and his Faraian partner, Mara ibn Durazzi, find themselves facing their own moral issues when they set out to eliminate a Faraian rebel leader. Will they be able to overcome their own minds--and each other--and get the job done? ("A Covenant of Shadows" is the sequel to this book.)