The true story of Captain Richard Phillips and the 2009 hijacking by Somali pirates of the US-flagged MV Maersk Alabama, the first American cargo ship to be hijacked in two hundred years.

A CIA operation to purchase classified Russian documents is blown by a rival agent, who then shows up in the sleepy seaside village where Bourne and Marie have been living. The pair run for their lives and Bourne, who promised retaliation should anyone from his former life attempt contact, is forced to once again take up his life as a trained assassin to survive.

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.