In the first book, The Bourne Identity , the title character suffers amnesia. Over the course of the book, he regains his memory with the help of a Canadian economist, Marie, and eventually finds out that his real name was Webb. He had previously been an operative of the Central Intelligence Agency in an elite project in Southeast Asia and Vietnam codenamed Medusa. Following the American forces' withdrawal from Vietnam, he joined Project Treadstone 71, where he was used as bait for the infamous European assassin Carlos the Jackal, and assumed the identity of a mock assassin, Jason Bourne.“Bourne" took credit for various kills in China and the rest of Asia, acting as a rival to the Jackal, in order to draw him out of hiding.
The story of The Bourne Supremacy is set during the British negotiated handover of Hong Kong to the People's Republic of China on the expiration of its ninety-nine-year lease on the New Territories.
Bourne has recovered from most mental and all physical injuries and is teaching Asian studies at a university in Maine under his real name of David Webb. He is also living happily on campus with Marie and is getting regular psychological tests from his doctor, Morris Panov.
Meanwhile, high-ranking U.S. officials 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 a Bourne imitator (“impostor"). The officials know Sheng Chou Yang to be a fanatical nationalist mole who they fear might trigger a war, and decide to use Webb to kill the Chinese official, but know of his mistrust of the U.S. government. Aware of Webb's deep-seated emotional instability due to the loss of his firstwife and children in Vietnam, they hatch a plan to abduct Marie and thereby force Webb to work for them.
A representative of the U.S. Government arrives and informs Webb of an imitator in Asia, someone who is killing under the name of Jason Bourne, a name feared in Asia because of the accredited kills during his work with Treadstone 71. Webb is told he requires a more visible security force because there is evidence someone wants him dead.
Soon thereafter, Marie is abducted by unknown men while Webb is at the university. 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 for him by the kidnappers. He turns to the only person he thinks will be able to help him, Alexander Conklin. Conklin is convinced there is government involvement but that they have lost control of the situation and the hired guns holding Marie are no longer in their control. Webb, who has transformed back into his hated persona of Jason Bourne, now has no choice but to go to Hong Kong and play out the scenario to get Marie back. There he meets with a man claiming to be a wealthy Tai-Pan who wants Webb to bring back the impostor Jason Bourne because the impostor killed his wife; the Taipan is played by a British intelligence officer collaborating with the CIA.
Marie, held captive in a British hospital, fakes an illness and escapes, taking refuge with Catherine Staples, a former colleague employed at the Canadian consulate in Hong Kong. She later contacts Conklin, who confronts Under-Secretary MacAllister and Ambassador Havilland, the orchestrators of the plan to manipulate Webb. Webb, tracing the impostor Bourne through Kowloon and Macau, encounters Echo, another former Medusa operative, who is also tracking down the impostor Bourne, whom he personally trained. They join forces and track the impostor to mainland China, where Echo is captured. Webb tracks him and the impostor to a meeting in a bird sanctuary, where Echo is executed by Sheng Chou Yang. Webb captures the impostor Bourne, but in attempting to swap the impostor for Marie, is misled by MacAllister, as Marie is still hiding with help from Conklin. Without Marie, Webb has stated clearly he will kill the impostor. Thinking Marie has been killed, Webb assaults Havilland's "sterile house" estate, where the impostor is killed and Webb nearly as well, saved only by the timely arrival of Marie and Conklin.
Webb is then told of the whole plan and why Havilland had to abduct Marie. Since Webb has seen what Sheng is capable of and possibly due to a dying wish of Echo, he says that he must go back into the fray and kill Sheng. McAllister goes with Webb, and during their search for Sheng, McAllister explains that he must be the one to kill Sheng, that was his plan from the start. The meeting between Sheng, Webb and McAllister takes place on the Chinese border, and during the meeting McAllister is shot before he can make the kill, so Webb has to kill Sheng instead. They escape with Sheng's helicopter.