What is the conflict to Maximum Ride the Angel Experiment?

The School is located in Death Valley, and the first half of the book takes place in the southwestern area. Later in the book, the setting moves to New York City.
There are many settings in the book. There's the flock's house up in the Colorado mountains, Ella and Dr. Martinez's house in Arizona, the School, New York, the Institute for Higher Living, and the sewers. Mostly, though, it takes place in New York and Colorado.