During the U.S.-led occupation of Baghdad in 2003, Chief Warrant Officer Roy Miller and his team of Army inspectors are dispatched to find weapons of mass destruction believed to be stockpiled in the Iraqi desert. Rocketing from one booby-trapped and treacherous site to the next, the men search for deadly chemical agents but stumble instead upon an elaborate cover-up that threatens to invert the purpose of their mission.

Bourne is brought out of hiding once again by reporter Simon Ross who is trying to unveil Operation Blackbriar, an upgrade to Project Treadstone, in a series of newspaper columns. Information from the reporter stirs a new set of memories, and Bourne must finally uncover his dark past while dodging The Company's best efforts to eradicate him.