In the prologue, CIA Deputy Director Martin Lindros is in Ras Dejen, the tallest peak in the Semien mountain range, tracking major shipments of yellowcake uranium and atomic bomb weaponry.

Back at the CIA, Bourne is introduced to a number of new people: Matthew Lerner (the Deputy Director until Lindros gets back), Soraya Moore (a senior case officer), Hiram Cevik (a prisoner, actually Fadi in disguise), and Tim Hytner (who is framed as a traitor to the CIA organization).

Unwittingly Bourne brings Cevik out of his prison cage to take a walk with him in an attempt to extract more information about Fadi.

Once the Hummer is stopped up the street, CIA officers surround the car, waiting for the prisoners to step out.

Later, Jakob and Lev Silver (Fadi and Muta ibn Aziz in disguise) arrive at the Hotel Constitution, located on the northeast corner of 20th and F Streets.

The dog (a boxer named Oleksandr) is with Soraya and she is there in Odessa to help Bourne, unaware that she was sent by the impostor Lindros to be killed as well.

Bourne and Soraya escape and end up in Istanbul, Turkey, where they find a tracking device planted on him.

They also discover the truth behind a lot of the other deceptions being played out, including the fact that Soraya's friend, Anne Held was Karim (The Fake Lindros)'s Mistress, and the true mole in the CIA.

They end up crashing, and Bourne finds out that he didn't actually kill Fadi's sister Sarah; Muta and his brother Abbud did because she was having a secret love affair, a mortal sin in Muslim tradition.

Bourne and his friend Feyd al-Sould, whose men kill Muta, find the underground opening to the Dujja facility in Miran Shah.

Fadi however, had managed to shoot a bullet through Lindros' jaw and eye socket, giving the injured CIA deputy director very little time to live.

They get shot at by terrorists in the Old Man's limousine, thinking that they can get into the headquarters by showing them the DCI's face, redone by another one of Fadi's men, which they'll blow up with C-4.

Bourne kills Karim al-Jamil at the IVT facility by using the same trademark as his nemesis Carlos the Jackal, a bullet to the throat.

However, after thinking about it he realizes that the second timer was put in there by Veintrop, who, to get back at Fadi and Karim's men for hurting and torturing his wife, didn't connect it to the bomb.