The Bourne Deception picks up where The Bourne Sanction left off. Jason Bourne's nemesis, Arkadin, is still hot on his trail, and the two continue their struggle, reversing roles of hunter and hunted.

When Bourne is ambushed and badly wounded, he fakes his death and goes into hiding. In safety, he takes on a new identity, and begins a mission to find out who tried to assassinate him. Jason begins to question who he really is, how much of him is tied up in the Bourne identity, and what he would become if that was suddenly taken away from him.