The second installment in Robert Ludlum's Jason Bourne series picks up years after David Webb, a former covert operative, has settled into academic life in Maine with his wife, Marie St. Jacques. Webb once assumed the identity of Jason Bourne, a mythical assassin created by a CIA project called Treadstone 71 to lure out the infamous killer Carlos the Jackal. During that mission, he suffered amnesia from gunshot wounds and was nearly killed by his own government before Marie helped him reclaim his identity. Now an associate professor of Oriental Studies, Webb endures violent flashes of memory from his past as Delta, his code name in Medusa, a clandestine military unit during the Vietnam War.
The novel opens in Kowloon, where a man disguised as a priest massacres five men in a cabaret back room, leaving a calling card in blood: the name Jason Bourne. Among the dead is the Vice-Premier of the People's Republic of China. At a secret compound in Colorado, Ambassador Raymond Havilland briefs Undersecretary of State Edward McAllister on the crisis. Someone has resurrected the Bourne legend to kill across Asia on behalf of Sheng Chou Yang, a Chinese minister of state who appears loyal to Beijing but is secretly the son of an industrialist tied to the Kuomintang, the Chinese Nationalist movement driven from the mainland after the Communist revolution. Sheng leads a conspiracy to seize economic control of Hong Kong through a fraudulent financial commission; when the scheme collapses, Beijing will send troops into the colony, with catastrophic consequences.
Havilland argues that only the original Bourne can hunt the impostor and use the assassin's channels to reach Sheng. Since Webb would never cooperate willingly, Havilland orders Marie's kidnapping to recreate the trauma that first transformed Webb into Delta: the murder of his Thai wife and children during the Vietnam War. McAllister delivers a fabricated cover story, claiming a Hong Kong taipan, or powerful business magnate, named Yao Ming wants Webb dead because the new Bourne killed his wife. Shortly after McAllister's visit, Webb's guards are withdrawn and Marie is taken. A bloody hand print appears on the front door, and a typewritten note on the pillow reads: "A wife for a wife, Jason Bourne. She is wounded but not dead, as mine is dead. You know where to find me, and her, if you are circumspect and fortunate" (60).
Webb contacts former intelligence officers, but each refuses to help. His psychiatrist, Morris Panov, discovers that State Department logs have been fabricated. Webb examines the evidence and concludes the kidnapping was staged by his own government: The hand print was made with a rubber glove, and the note was typed on his own typewriter. Marie manages a satellite call from a plane over the Pacific. She is unharmed and tries to send a coded message about "my favourite tree" (153), the maple, meaning Canada, but her captors take the phone and order Webb to the Regent Hotel in Kowloon. Before departing, Webb confronts Alexander Conklin, a former CIA strategist who once tried to kill him. Conklin recognizes the operation has lost control and pressures the State Department while spreading the false story that Marie escaped. At the airport, he urges Webb to become Jason Bourne again.
In Hong Kong, Webb dismantles the enemy's network. He intimidates the Regent Hotel's assistant manager, who was recruited to funnel him into a surveillance suite, and extracts a telephone number. He arms himself through the Mongkok district's underworld. When he confronts the assistant manager on a harbour walkway, gunfire from above targets not Webb but the hotel man, the expendable contact. Webb later speaks with Marie by phone; her strained voice again references "that lovely street with the dark green trees, my favourite tree" (153) before she is cut off. He is instructed to meet a taipan in the Walled City of Kowloon, a lawless slum beyond police jurisdiction. Disguised as a laborer, Webb neutralizes the guards and confronts the taipan, who demands that he hunt the impostor and deliver him alive. After Webb leaves, the man reveals himself as Major Lin Wenzu of MI6, working under Havilland.
Meanwhile, Marie escapes the hospital where she was held by faking neurological symptoms. She reaches the Canadian consulate and enlists Catherine Staples, a senior officer she knew from Ottawa. Staples's sources confirm McAllister's entire story was fabricated: No taipan named Yao Ming exists. She hides Marie in Tuen Mun, a town in the New Territories.
Webb works through the taipan's list of underworld contacts and learns the impostor can be reached through a Macao casino using original Treadstone codes: "Cain is for Delta and Carlos is for Cain" (198). He follows the impostor across the Chinese border but loses him when the killer boards a government jet. At Kai-tak Airport, Webb infiltrates security and discovers the impostor has planted a bomb in the lead limousine of a motorcade carrying Chinese delegates who are Sheng's political opponents. Webb alerts police, and the vehicle is evacuated seconds before it explodes. At the Kam Pek casino in Macao, Webb contacts the impostor's relay system and reaches a meeting in Guangdong province. There he witnesses a failed ambush and tackles Philippe d'Anjou, his old Medusa comrade code-named Echo. D'Anjou reveals he created the new Bourne: a psychopathic former British Royal Commando whose appearance was surgically altered. The creation broke free and accepted contracts from Sheng. D'Anjou pledges to help.
Havilland reveals Sheng's conspiracy to Staples, who agrees to help retrieve Marie, but Sheng's agents assassinate Staples after penetrating Lin's operation and stealing the classified Sheng dossier from the Victoria Peak safe house. Lin identifies the mole and kills him but is severely wounded. Marie, spotting McAllister near her hiding place, flees Tuen Mun and is rescued by sympathetic residents who disguise her with aged grey hair.
Webb and d'Anjou track the impostor to Beijing. At Mao's Mausoleum in Tian An Men Square, Webb walks into a reverse trap but escapes by shooting the crystal coffin of Chairman Mao, creating a stampede. D'Anjou is captured. At the Jing Shan Bird Sanctuary outside Beijing, Sheng presides over a torchlit ceremony, executing prisoners with a ceremonial sword. D'Anjou, among the captives, provokes Sheng with insults to buy Webb time and is killed. In the ensuing chaos, Webb captures the impostor and escapes.
Back in Hong Kong, Webb launches a one-man assault on the covert safe house on Victoria Peak, planting explosives and setting it ablaze. The impostor breaks free and kills marines before a guard shoots him dead. Marie, brought to the house by Havilland, runs onto the burning patio. Deep in the Delta persona, Webb does not recognize her. She stands in his line of fire: "You're Jason Bourne! You're Delta! You're anything you want to be, but you're also mine! You're my husband!" (577). Panov breaks through the cordon and tells Marie to stay back; David must come to her. Trembling and weeping, Webb drops his weapon and runs into her arms.
Webb agrees to return after recognizing Sheng's photograph as the butcher from the bird sanctuary. McAllister insists on accompanying him, having rejected hired assassins as traceable and prepared sealed documents framing himself in a personal blood feud with Sheng. They cross into China, where Webb poses as the impostor to lure Sheng to a rendezvous in the Guangdong hills. Sheng arrives by helicopter, reveals his fanaticism, and shoots McAllister. Webb charges with a knife and kills Sheng.
They escape in the commandeered helicopter. McAllister delivers the recovered dossier and is appointed chairman of the National Security Council. Lin survives his wounds. Webb and Marie fly to Hawaii with Panov and Conklin. On the beach, David asks what one does with a part of oneself that one loathes. Marie answers: "Accept it . . . We all have a dark side, David . . . Perhaps we can't exist without it" (679).