In the first book, The Bourne Identity, Jason Bourne had suffered amnesia. Over the course of the book he regained his memory with the help of a Canadian economist, Marie St. Jacques, and later found that he was previously a special operative for the United States Government in an elite project in Southeast Asia and Vietnam codenamed Medusa. After a tragic accident involving the death of his family, he joined Project Treadstone Seventy-One, where he was given the code name of Cain and used as bait for the infamous European assassin, Carlos. Bourne took credit for various kills in China and the rest of Asia, acting as a rival to Carlos, in order to draw him out of hiding and into the hands of the U.S. Government. In a climactic scene at the end of the book, Carlos escaped and Bourne was almost killed as he was believed to be a traitor by his uninformed employers.

At the beginning of The Bourne Supremacy, Bourne has recovered from all his mental and physical injuries, and he is teaching Asian studies at a university in Maine under his real name of David Webb. He is also living happily near campus with Marie and is getting regular psychological tests from his doctor, Morris Panov. He is also being closely guarded by the CIA.
It is then that Edward Newington McAllister, the Undersecretary of State, arrives and informs Webb of an imitator in Asia, someone who is killing under the name of Jason Bourne, later to be revealed as the son of a British revolutionary named Alcott-Price, a name feared in Asia because of the accredited kills during his work with Treadstone 71. Webb refuses to assist the government.
Some time after this discussion, Webb's security guards abandon him on orders from unknown superiors. Webb suspects something is wrong, so he rushes to his house only to discover his wife has been abducted. He 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 returns to Asia in an attempt to find Marie after a hint found in his house. There he is told by a wealthy "Tai-Pan" that he is to find and capture the fake Jason Bourne, without killing him, in exchange for his wife. Unbeknownst to Webb, the Tai-Pan is actually a MI6 operative whose motive for capturing the fake Jason Bourne is to find a way to Sheng Chou Yang, a top Chinese government official who plans a revolution in China. The American State Department and MI6 are working together to kill Sheng before his plans for revolution can be carried out, and they have reasoned that the only way to do this is to use the original Jason Bourne to capture the fake Jason Bourne, a hired assassin of Sheng. The plan is masterminded by an Ambassador Havilland, using the analytical undsecretary of State Edward McAllister and an MI6 operative Lin Wenzu.
However, Marie St. Jacques-Webb outsmarts her bureaucratic captors by feigning illness. She escapes a Hong Kong hospital and eventually makes it to the Canadian consulate, where she recognizes a name from the list of staff. After Marie's escape, Wenzu puts out an alert to all Hong Kong police to capture Marie. Marie finds her friend, Catherine Staples first and Staples puts her under her protection, while doing some digging they discover parts of the State Department and MI6's plans. Staples is captured by Wenzu's team and is told the whole truth by Ambassador Havilland. St. Jacques-Webb senses that something is wrong when Staples doesn't contact her at the time she indicated, so Marie flees her hiding spot, almost being captured but escaping into an unknown city. There, two young hoodlums attempt to rape Marie, but she fights them off. The citizens of the town discover the horrible act against Marie, and do all they can to help Marie evade the authorities, even creating a spontaneous parade to create confusion. Marie escapes and is able to contact Alexander Conklin. Conklin rushes to Hong Kong with Morris Panov, the Webb's psychiatrist, and there they mount a plan to confront the State Department and draw Bourne/Webb out and back to safety.
Meanwhile, David Webb/Jason Bourne maneuvers through an elaborate system of couriers and messengers, all leading to a mysterious Frenchman who Bourne thought could take him to the imposter. He defeats one of these couriers in hand-to-hand combat, and the courier becomes an ally, leading Bourne to a jungle where he witnesses an unknown man attempting to kill the fake Jason Bourne. The unknown man fails, and the fake Jason Bourne escapes, but Bourne discovers that the unknown man was actually Phillipe d'Anjou, a friend from long ago during Operation Medusa, and more recently a contact in Paris at Les Classiques. d'Anjou, revealed to be the mysterious Frenchman, and Bourne team up to hunt down the fake Bourne, and it is revealed that it was d'Anjou was the one who taught the fake Bourne many of his tricks, but the fake Bourne severed his ties with d'Anjou, and began to work for another person, a wealthy Tai-Pan perhaps.
Bourne and d'Anjou learn that one of the imposter's targets is a Chinese diplomat who will be arriving at a nearby airport after concluding negotiations with the British delegation. d'Anjou and Bourne infiltrate the security around the airport, and after a tense hour of going over possible assassination possibilities, Bourne figures that the imposter will kill an entire group of diplomats. Limousines carrying the diplomats are ordered to stop, and Bourne orders everyone out of the first limousine seconds before it explodes, thwarting the imposter's plan. Bourne then spots the imposter escaping, but is unable to stop him.
The rest of the book consists of two side-by-side stories, one of Webb-turned-Bourne trying to track down and kill the target, and the other of Marie trying to escape and find Bourne in order to tell him the truth. The story unfolds as an ancient cult and ritualistic murders become a part of the revolutionary's plan.
The story is set during the expiration of the 100-year contract for the British ownership of Hong Kong. Southeast Asia is particularly volatile and fragile, and mistakes cannot be tolerated by any world power.