After the events of Maximum Ride: The Angel Experiment, the flock is headed toward Washington, D.C., where they hope to find the answers to their origins. However, after Fang is gravely injured by Ari and taken to a hospital, the flock is taken in by an FBI agent named Anne on the agreement that she is allowed to examine them. The flock enjoys a rare period of peace, but there are sinister things at work in the background. A major multinational corporation named Itexicon (Itex) is plotting to destroy the world, based on what Angel overhead when she was kidnapped back at the lab, and is also tracking down the flock's movements. Anne reveals herself as the leader of the lab that created the flock and seeks to recapture them. Furthermore, Max must face her worst adversary yet--her own clone.