Black Flagged by Steven Konkoly
Book One in the Black Flagged series:
A graduate of the Department of Defense's experimental Black Flag program, Daniel Petrovich carries a secret he's taken extreme measures to keep buried. A secret hidden in the deepest vaults of the Pentagon.
Someone is trying to raise the fallen program from the ashes and bring Daniel back with it. Someone who holds the key to Daniel's darkest secrets...and has pulled his strings before.
In exchange for the promise of a clean slate, and a chance to keep the life he has built with the woman he loves, Daniel agrees to carry out one final mission: the seemingly uncomplicated assassination of a confirmed terrorist financier.
Daniel's life is about to disintegrate, as he becomes the focus of a relentless federal manhunt, and the target of a ruthlessly vengeful CIA agent. To survive, he'll be forced to release a dark side he'd fought for years to suppress. A dark side critical to his former puppet master's intricate plan to revive the Black Flag program.