It's been two years since Jason Bourne (MATT DAMON) was pulled from the sea with two bullet holes in his back and a case of amnesia, only to eventually discover that he was a covert government operative trained to assassinate others. Having successfully eluded other assassins and his former director's attempts to have him killed, Jason now lives in India with
Marie (FRANKA POTENTE) the woman he met on his path of self-discovery.
Yet, he's still troubled by mysterious visions and nightmares about his former life. He doesn't have much time to think about them, however, as another assassin, Kirill (KARL URBAN), seriously disrupts his life and sends him on the run once again. He has bigger worries, however, as he's been framed for the murders of two U.S. agents who were trying to obtain missing records about a murdered Russian politician.
With Jason's fingerprint conveniently showing up at the crime scene, CIA deputy director Pamela Landy (JOAN ALLEN), who was in charge of those two murdered agents, wants to know who and what Bourne is. With fellow agents Ward Abbott (BRIAN COX) and Nicky (JULIA STILES) assigned to the case -- both having a knowledge of the rogue agent that may lead to his capture -- Jason tries to figure out who framed him and what his visions and dreams mean, all while avoiding being captured or killed.