When the Russian president gets kidnapped in a coup, an American submarine captain leads a rescue mission in the hopes of avoiding all-out war.

In 1980s Beirut, Mason Skiles is a former U.S. diplomat who is called back into service to save a colleague from the group that is possibly responsible for his own family's death. Meanwhile, a CIA field agent who is working under cover at the American embassy is tasked with keeping Mason alive and ensuring that the mission is a success.

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.