Specials is the third book in the Uglies series.
The story begins after Tally Youngblood has become a member of an advanced group of Specials, called Special Circumstances; the Cutters, led by Shay, to whom they refer to as "Boss." Other members of the group include Tachs, Ho, and Fausto.
The Cutters, in Ugly disguises, go undercover at the Uglies' Spring Bash, looking for members of the Smoke. Shay begins dancing with an Ugly boy, until everyone is dancing. Distracted from the other Cutters, the other four search for Smokies (rebels). Soon, Tally spots a girl slipping a boy a pack of pills. Using their skintenna connection, implanted chips that allow Specials to communicate with each other from remote places and transmit sounds, Tally contacts the other Cutters, and they all go after the girl. They follow her on hoverboards out into the woods, where they are ambushed by Smokies in sneak suits and wielding electrified arrows.
David, who is with the other Smokies, stuns Tachs, and tries to escape with Tachs' unconscious body. Shay tries to stop him, but is stunned as well, and David, along with the others, escapes on the Cutters' hoverboards with Shay and Fausto. Tally takes Ho's board when he arrives, and rushes off after them. Eventually, she finds David hovering above the river with Shay, waiting for her. They try to ambush Tally again, but she stops them, so David throws Shay's body into the water. Tally rescues Shay just in time. Tally finds out later that the pills were meant for Zane, and is upset that Zane has been transferred back into New Pretty Town instead of in the Cutters. Tally manages to convince Shay to help her devise a plan to get Zane to become a Special.
Together, they infiltrate the city's armory to get an alloy cutter, as Zane is now watched through an interface chain that could not be removed. In the process, they destroy the armory by releasing nanos that were meant to be Hunger. They then assist Zane in running away to the Smoke with the Crims, hoping that the city's authorities would think that Zane was behind the armory's destruction. They both follow Zane to the Smoke, planning to pretend to capture him once he arrives, bringing him back to the city and convincing Dr. Cable to make him Special.
Zane and the Crims depart from the city soon after and meet up with Andrew Simpson Smith who gives them a position finder to the Smoke. Tally also meets Andrew Simpson Smith, who had escaped out of the preserve by burning the "little men". Andrew had been working for the Smokies handing out position finders so run-aways could reach the Smoke. Tally and Shay get into an argument, so Tally gives Shay the position finder so Shay can fly ahead to the Smoke.
Tally tracks the Crims for a while down south. While tracking Zane and the Crims, Tally falls for a trap laid by Zane, by luring her in while he was pretending to sleep and he confronts her about following them the whole way to the Smoke. During this exchange Tally and Zane kiss but Tally's Special brain can't stand Zane's shakes due to his brain damage from the pills in the second book, and so Tally runs away from him. Shortly after their meeting the Crims reach the end of the trail set out by the position finder and soon realize that it is only an extraction point to the real New Smoke. At the extraction point a helicopter arrives and takes the Crims away and Tally hitches a ride on the helicopter to the New Smoke.
After a short while the helicopter reaches the New Smoke, which actually turns out to be the city of Diego, one which allows a greater variety of "looks" for the Pretty operation and does not include the lesions. There Tally is confronted by Fausto, who tries to inject Tally with a Special cure Maddy had developed. Tally runs away, and is cornered at a giant cliff. Tally jumps off, using her crash bracelets to stop her fall, which brutally injures her. In her weakened state, she is captured by city authorities or wardens who look like bogus bumble bees, who lock her in a padded cell. She is told that she cannot leave until they operate on her, telling her that the artificial alterations to her body qualify her as a dangerous weapon, and weapons are illegal in Diego. As Tally is about to go under the knife, she is rescued by Shay, who had been given the cure. Shay convinces the others to allow her to stay Special, because Tally will be able to help, as Diego and Tally's city are engaged in a battle. Tally's city's hovercars attack the city until it is helpless, but then cease fire. Tally learns that Dr. Cable, who has full control of Tally's city, planned to take over the city and give everyone the lesions once more.
Tally goes to the Hospital to see Zane, who had been there since they arrived because of his brain damage. The doctors explain that they had tried to cure him, but it had gone seriously wrong, and had left Zane in a vegatative state. Tally was extremely mad and stricken with sadness, but it was Zane who gave consented permission. The doctors need Zane's bed, so Tally says her last goodbyes, and they take him off life-support.
Tally travels back to her city to explain it was her and Shay who broke into the armory, not Diego, like the city thought. She rests in the Rusty Ruins first, where she meets David, and is given the Special cure injector. She goes into her city, where Dr. Cable explains that she knew it was Tally all along who had broken into the armory, that they used it as an excuse to attack Diego. Tally comes up with a plan, and lies that at Diego, she was made into a living camera, and was recording every word Dr. Cable said, and that the injector was an antenna, and all Tally had to do was push "send." Dr. Cable runs forward and knocks the needle off the injector with her hand. Dr. Cable smiles, oblivious to the fact she had just been given the cure. Tally is taken to a prison cell, and is then taken to an operating room to be made normal, because the Council think Specials are psychos. She is rescued at the last second by a normal Dr. Cable, who claims that she rescued Tally because she wants at least one of her "creations" to live on.
Tally meets David back in the ruins, where she receives numerous pings. She writes back to Shay, Maddy, and Peris, saying she and David will stay out in the wild; and as the cure for the lesions spread around the world, they'll both be there "to remind them of the price the Rusties paid for their freedom and going too far." She ends by telling them all to "be careful with the world, or next time we meet, it might get ugly."