I read this sometime after watching the third Bourne movie. They really have nothing to do with each other, beyond the titular character. Marie's still there and has the same basic role, but she's a professional at a conference that gets interrupted, IIRC. A few characters have the same names as the ones from the movie but all their functions are different. This is about post-Vietnam shenanigans, which I actually found quite intriguing. Bourne's been undercover for way too long trying to find an assassin, something happens, he loses his memory, etc. The writing is simplistic and the characters come off kind of wooden.
Edit: Because this really bugged me in the book. In the movie, Marie stays with Bourne because they're in it together. In the book, she decides to stay and help Bourne because(show spoiler)