The film follows the storyline of the novel, with a run-time of 3 hours 5 min. With commercials added, the running time was extended to four hours, and the film was first shown on ABC in two two-hour installments over two nights.
The film's plot exhibits some differences from that of the novel. The undercover identity of Jason Bourne is simplified. In the book, David Webb, because of his amnesia, believes himself to be Jason Bourne and an assassin called Cain. In the film, the name Cain is left out. In the film, Carlos is shown to be responsible for killing Webb's wife and child, which is not the case in the novel. In the book's ending, Carlos escapes in the confusion, whereas in the film he is gunned down by David Webb.