Jason Bourne has recovered from most of his mental and physical injuries and is teaching Asian studies at a university in Maine under his real name of David Webb, living happily on campus with his wife Marie under supervision of psychiatrist Morris Panov.

Meanwhile, high-ranking U.S. officials Ambassador Raymond Havilland and Undersecretary Edward McAllister discuss an increasingly alarming situation in the People's Republic of China, where the popular Communist official Sheng Chou Yang is boosting his rise to power with assassinations perpetrated by someone impersonating Jason Bourne.

Webb returns to the house, finds clues to her abduction, and immediately phones government officials, threatening to leak information about Treadstone and Medusa in an attempt to get assistance.

He finds out information has been manipulated in order to make him seem crazy and delusional, and that his only course of action is to follow the instructions left by the kidnappers.

Marie, held captive in a British hospital, fakes illness and escapes, taking refuge with Catherine Staples, a former colleague now employed at the Canadian consulate in Hong Kong.

Webb tracks him to a bird sanctuary at night, where Sheng Chou Yang is seen holding an open air conference with his rebel supporters and captured "traitors" to his cause, whom he is going to "judge", including Echo and the impostor Bourne.

The meeting between Sheng, Webb and McAllister takes place on the Chinese border with the assistance of Wong, a previous acquaintance of Bourne.