With the climactic events of The Bourne Ultimatum behind him, Jason Bourne is able to once again become David Webb, now professor of linguistics at Georgetown University. However, this serenity does not last for long and, when a silenced gunshot narrowly misses Webb's head, the Bourne Persona reawakens in him yet again.
Bourne's first objective is to get to his long time friend and handler at the CIA, Alexander Conklin.
However, unbeknownst (as yet) to Bourne, a Hungarian by the name of Stepan Spalko has now drawn Jason into a web—one which he cannot escape as easily as his professorial façade.
Finding Alex dead along with Doctor Morris Panov, Bourne realizes the trap as soon as he hears the police arriving. With his car outside and his fingerprints in the house, he immediately understands that he has been framed.
So, with only Conklin's cell phone and a torn page from a notebook to go on, Jason Bourne sets off to find out who's trying to kill him and who killed his friends.
After warning Marie and his kids, Jamie and Alison, to proceed immediately towards their safe house, he slips through the CIA cordon and makes his way to an independent agent who was talking to Alex Conklin when he was killed. Having received travel plans to Hungary and a mission to meet Janos Vadas, Conklin's contact in Hungary, he proceeds to unravel the truth behind why Alex and Morris Panov were killed.
Meanwhile, a group of Chechen terrorists have been fighting a losing battle against Russian invaders when a man named Stephan Spalko appears to solve their problems. Spalko, we later discover, had Conklin and Panov killed and kidnapped a Doctor Felix Schiffer. Schiffer is an expert in bacteriological particulate behaviour.
Spalko intends to release a bacteriological weapon during peace negotiations between many World Leaders to be held at the Oskjuhlid Hotel in Reykjavík, Iceland, using the terrorists he is cultivating as a diversion. The book charts Bourne's course from the United States, to France and then to Budapest in Hungary where he learns the final thing he needs to do—to stop Spalko's attack in Iceland.
This of course, has to be done with a CIA sanction out for him to be immediately terminated, as he is believed responsible for the deaths of Conklin and Panov.
There is also the matter of Spalko's hired assassin, Khan, who is preternaturally able to track Bourne where everyone else cannot. Khan is revealed to be the Bourne Legacy; he is Joshua, David's son from his first marriage, who believes erroneously that he was left for dead by his father in Vietnam. Bourne, however, refuses to believe that Khan is Joshua, convinced that Joshua was killed decades ago, and continually tries to avoid him and the truth.
Though Khan is at first working for Spalko, he eventually realizes that he has been used as a pawn in Spalko's personal game. After revealing later on to Bourne that Annaka Vadas, the daughter of Janos Vadas, is a traitor, he begins to feel that Bourne is not the hateful father that he had imagined.
Unfortunately, Bourne is still unable to believe Khan is Joshua—until he hacks into the CIA database and discovers that Joshua's body had never been found. In a fit of rage, he attacks Khan, first believing that it is a conspiracy to hurt him, but is later captured by Spalko.
After rescuing Bourne from Spalko, Khan makes an uneasy peace with his father. While on the plane to Iceland, however, Khan reveals a piece of information that finally convinces Bourne that Khan is his son. After subsequently revealing that he (Bourne) lost his memory while undercover as Cain, Khan begins to rethink what his views regarding his father are.
After completing the operation and stopping Spalko, Khan—Joshua—makes up with his father and realizes that his hatred was always a reflection of his personal struggles and that, in truth, he truly loved Bourne. He requests Bourne, however, not to reveal his identity to Marie, in whose life he feels he has no place. At the end of the novel, Joshua reminds Bourne with a simple gift that as long as David Webb is Jason Bourne, he (Joshua) will always be there.