"He dreamed that Aaron was mourning for him. That Aaron missed him, just as Alex longed for Aaron. That they met again, and Aaron was so glad to see him. That Aaron wrapped his arms around his brother and said how terribly, awfully sorry he was that Alex was Unwanted, and that there had been a mistake-but that they thought it was too late, that Alex was already dead." Page 132
Alex and Aaron are twins living in a nation where creativity is against the law. The high priest Justine has a policy in which 12 year olds are deemed "Wanted" and become a member of the society, or "Unwanted" and are executed. Because Alex has committed a creative offense and Aaron hasn't, the two are seperated from each other.
As Alex and the other Unwanteds are driven to the execution area, the Great Lake of Boiling Oil, they discover that the seemingly awful place is actually a magicalsafe haven for Unwanteds that has been run by a wizard by the name of Mr. Today. Alex gets to know three other Unwanteds: Samheed, Rachael, and Lani.
The new Unwanteds are sent to an academy on the land to get training in creative magic in case of attack by the nation they came from led by High Priest Justine. The school is very nice and even has nice dorms, but Alex still longs to see his brother Aaron.
Mr. Today ends up hearing about Alex's longing for his twin and begins holding him back in his lessons so he doesn't reveal the safe area to Aaron, who now works with High Priest Justine. He begins secluding himself from his friends so he can learn by himself as to how he can get to Aaron. After spying on Samheed in the library, he learns how to make a magic door to his twin.
Alex finally get caught up in his lessons and contacts his twin, but Aaron reports all that Alex told him about the safe haven. High Priest Justine ends up bringing her forces to the place, forcing the Unwanteds to fight them off with their creative magic.
The Unwanteds triumph over High Priest Justine and start the nation with a blank slate, restoring the city's color and creativity. Lani reunites with her father, and , although he is upset that he lost his high government position, Aaron is happy to be with Alex again.