The Bourne Ultimatum is a novel about the complex machinations of Cold War intrigue. It begins with the discovery by Carlos the Jackal that his old nemesis, Jason Bourne, was not killed thirteen years ago in Hong Kong, as had been widely publicized. In fact, he is living in Maine as David Webb, a university professor. Carlos, fed by his hatred for Bourne, whose existence had clouded his self-proclaimed title of the "world's greatest assassin," fires the first salvo in a murder attempt against David's friends and mentors, Alex Conklin and Dr. Morris Panov. David immediately fears for the safety of his family and allows his alter-ego of Jason Bourne, cold blooded killer, to emerge. The novel deals with their conflict culminating in the surprise death of Carlos, the Jackal.

Jason, once a member of a Viet Nam era killer squad, code named Medusa, discovers that the organization has re-emerged in the civilian world. Although he sees no connection between the new Medusa and Carlos the Jackal, Bourne sees it as an opportunity to have the organization hire Carlos to kill him, thus bringing the Jackal out of his cover in Paris.

Jason's family goes to the island inn called Tranquility, owned by Marie Webb's brother, John St. Jacques. Nevertheless, Carlos manages to locate them and form a plot for their extermination. Jason arrives and manages to foil the Jackal but gets seriously wounded in the exchange. The Jackal challenges him to come to Paris, as he makes his escape.

Meanwhile the CIA has become interested in the new Medusa and the director, Peter Holland, refuses to offer any assistance to Jason. Furthermore, he wants Jason to return to Langley to help in nailing the members of the new Medusa. Jason, however, continues on to Paris and is soon followed by his wife, Marie. Again, encounters with the Jackal end up in frustration. The fifty-year-old Bourne and the ailing sixty-year-old Jackal are determined to annihilate one another. Through a series of discoveries, bribery and deceit, Jason manages to come close to Carlos but never gets near enough to kill him. Meanwhile, the CIA relents and arranges the assistance of Dimitri Krupkin, a high-ranking Komitet Bureau agent. They fool Carlos into believing his contact in Moscow has been discovered, so the Jackal is off to Russia, believing that Bourne has finally been killed. Carlos has resentment against Novgorod, the Soviet espionage-training center where he himself was trained, because they had planned to liquidate him because of his insanity.

In Russia, the Jackal learns that Bourne is both alive and inside the Soviet Union. In an attempt to kill Jason, Carlos gets wounded but gets away to head for Novgorod. Krupkin arranges for Jason to be allowed entry into the top-secret center, and he locates Carlos for one final confrontation. In a twist, it is neither Carlos who kills Jason nor Jason who kills Carlos. Benjamin, American educated Russian young men, does the final deed that eradicates Carlos the Jackal.