The Bourne Supremacy follows an amnesiac protagonist, David Webb/Jason Bourne, and his long-suffering Canadian wife, Marie St. Jacques Webb, through misadventures in Asia as puppets of the U.S. government.

A spectacular assassination of a high-ranking Chinese official in Hong Kong suggests that the legendary hired killer, Jason Bourne, has come out of retirement. Officials from the U.S. CIA and State Department, who created the original myth years ago, know better, and know that if the assassin continues his work, Asia will be plunged into economic chaos and perhaps warfare. If that happens, all nations including the U.S. will have to take sides, and World War III could result. Fearing David Webb, a professor of Oriental studies in a small university in Maine, will not again accept the role of Bourne, codenamed "Delta" and "Cain" in earlier black operations, the government instead kidnaps his wife, Marie, to force the point.

The Delta persona rapidly takes control, and having enlisted the help of an alcoholic CIA agent in Washington, Alex Conklin, Webb/Bourne flies to Hong Kong, where he meets with the vengeful taipan, who claims false-Bourne has murdered his wife. He demands that the real Bourne find and capture the killer. Marie will then be freed. The taipan turns out to be the chief of British Intelligence (MI6) in Hong Kong, working for the Americans, who are led by Undersecretary of State Edward McAllister. The strategy unravels when Marie feigns illness to get admitted to a hospital and then escapes. Webb/ Bourne has insisted he must hear her voice when he returns with his prisoner. Finding her becomes a major part of the Anglo-American business and draws in a new boss, the amoral Ambassador Raymond Havilland.

Forbidden to enter Macau, Webb/Bourne follows false-Bourne's trail there. He meets an old friend from Operation Delta, a Frenchman who had been "Echo" to his Delta. Philippe d'Anjou is also the creator of false-Bourne, a project needed to support him in his old age. The psychotic ex-commando has cut him off, so d'Anjou is willing to help Webb/Bourne find him. Together they thwart an attempted assassination of the Crown governor at the Hong Kong airport and then follow the assassin into the People's Republic of China (PRC), when he is summoned to explain his failure. They track him to Beijing, where Webb/Bourne discovers the assassin has drawn him into a trap. After spectacularly shooting his way out of Chairman Mao's Mausoleum, Webb/ Bourne resumes the hunt, alone, because d'Anjou is kidnapped in Tian An Men Square.

The trail leads to a bird sanctuary where a top-level conference is to be held. Webb/Bourne infiltrates the grounds and watches in horror as a savage, Hitler-like madman tortures and kills the supposed traitors, who foul up the airport mission. D'Anjou is among the prisoners, and gives his life that Webb/Bourne might kill the assassin - and his tormentor. Webb/Bourne captures false-Bourne, smuggles him back to Hong Kong, and places the pre-arranged phone call to exchange him for Marie. Being put off and realizing that he has been traced, Webb/Bourne assumes Marie is dead, snaps mentally and drags his prisoner to the U.S. consular mansion intending to take maximum revenge on the puppet-masters. He does a spectacular military job.

Aided by an old friend in the Canadian consulate and later by Conklin and Panov, Marie, disguised as an older woman, arrives at the house and intervenes. Only slowly does Webb/ Bourne recognize her. Told the truth about his mission and shown the dossier on the man behind the world-menacing plot, Webb/Bourne recognizes Sheng Chou Yang, Echo's murderer. He volunteers to return to the PRC, taking along McAllister, a milquetoast diplomat who knows Sheng and believes he can get close enough to kill him. In a field in China, they confront their enemy, kill him, and plant incriminating evidence on his body. Having saved Asia and the world, the Webbs are allowed to resume a normal life.