The Bourne Sanction by Eric Van Lustbader

The Bourne Sanction - Jason Bourne has returned to his alter ego, David Webb. His current mentor Professor Specter, knowing his unusual talents, asks Jason to investigate the murder of a young man carrying information about a terrorist group’s activities. Meanwhile, Central Intelligence, which is going through its own upheaval, has come across murmurings of the Black Legion.

This book has so many twists and turns, and people changing sides, or rather under cover, from beginning to end you almost need a score card to determine who is fighting for whom and for what cause.