Ultimately, The Bourne Ultimatum is about a search for self-knowledge.
Although he focuses on killing Carlos the Jackal, Webb/Bourne searches for his own identity as he races around half the world in pursuit of his obsession. He is certain that for his family to be safe, he must kill Carlos, who is determined to avenge himself by destroying everything Webb/Bourne holds dear. A megalomaniac, Carlos is angry not only because Webb/Bourne has outwitted him in the past, but because Jason Bourne's reputation as an assassin almost eclipses his own.