The flock attend Ari's funeral, just after a new breed of Flyboy attacks the cabin they were thought to be living in. The flock are led by Dr. Martinez, who is Max's mother, and Jeb to Washington where they are offered a comfortable life and an education in return for service to the government. When an unexpected bomb goes off in their "safe house", Fang is very protective of Max. That night Dr. Martinez questions Fang and Max's relationship, but Max denies that anything is happening. Later, Fang comes in Max's room and they go out for "a fly". Fang tries to get Max to tell him what she wants from him, but Max doesn't want to talk about it. He gives up, calls her "such a pain" and kisses her. Max enjoys this, thinking that she loves "it" (the kiss) and loves "him" (Fang). But still not completely sure how to show her emotions, she runs away again, leaving Fang on the dock, again.
Max refuses the government offer and facility and they leave Washington. The flock members have also begun to mutate on their own, or without the abilities programmed in. Angel develops a shape-changing skill, Nudge develops magnetism, Fang develops the ability to disappear (can blend in to whatever is behind him if he stands still for long enough), and Iggy finds he knows what color things are by touching them. Meanwhile, it is revealed that the new breed of Flyboy, who are lumpy and misshapen, were created by a cybernetic man called the Uber-Director, or UD by Max. The head lieutenant is a powerful new Flyboy called Gozen. Dr. Martinez takes the flock to meet a woman named Brigid Dwyer, who offers them a comfortable life for nothing. Max doesn't believe her and asks her to show her what the flock would have to do. They are offered a place on a research ship which is on its way to the Antarctic, the flock accept and are soon on the bottom of the world. When they get there, two new, very unexpected skills develop. Iggy begins to see, but soon realizes he can only see things if they are surrounded by white, and Total grows wings.
During the trip, Max becomes jealous and is hurt when she finds Brigid and Fang getting closer. At one point Max gets so frustrated she abruptly jumps off the ship. A member of the research ship is attacked by a Leopard Seal and killed. The flock discovers that she was a spy sending information from the vessel. Angel goes off with Total and the love of his life, Akila, a Malamute brought along on the Antarctic expedition. Angel falls down a crevasse but is soon rescued by Fang and Max, who are in turn captured by Gozen. The rest of the flock was also captured and they are taken to Miami, which has been evacuated because of a Category 5 hurricane that is about to hit. They meet the Uber-Director (or "UD"), who attempts to auction them off to worldwide bidders, but the building they are in is destroyed by the Category 5 hurricane. Gozen and the UD are both destroyed, but the rest of the Flock survive, along with Akila. The ending consists of Max standing before Congress in Washington, D.C. pleading for the planet to change its ways. The flock is given a comfy life and a School dedicated to them. Max complained that School was the wrong word to pick, but before the flock can even enjoy it, the Voice inside Max's head speaks up and tells them that their mission is not over. The book ends with the Flock launching into the sky, with Max saying they can face any challenge that they come across.