While trying to escape the Specials’ invasion, Tally runs into the Boss, the librarian she met earlier with Shay. He gives her a bag of old magazines—a representation of hundreds of years of Rusty history—and says he will distract a nearby Special with a can of powdered habanero pepper so she can make a run for it. Then, seeing she is barefoot, he changes his mind. She won’t make it to the forest’s cover. Tally must distract the Special so he can get away. She tries to run for the Special with the canister, but the Special ducks away with superhuman agility. The operation has done more than make Specials look terrifying, Tally realizes. Before the Special can go after the Boss, Tally manages to kick the canister open and run away. The Special screams, an unnerving sound that raises the alarm amongst her fellows. They lead her away and find Tally hiding in the forest.
Tally is taken to a pen of “armed resistors,” where she encounters Croy and Shay. Shay is convinced that Tally has betrayed the location of the Smoke to the Specials—that this is why she came all along. Tally denies it. After all, she has destroyed the locket. True, she was a spy, but she didn’t betray her friends in the end. Specials march among the Smokies, scanning their eyes for identification and separating them according to city. When they scan Tally’s eye, they recognize her and congratulate her on her achievement in outing the location of the Smoke. Shay is vindicated; Tally is taken to the library to see Dr. Cable.
Dr. Cable is as disagreeable as ever, despite her success at finding and invading the Smoke. Suspicious of Tally’s initial resistance to the Specials, she demands to know where Tally’s locket is. If the locket had been damaged, she says, it would have sent out an automatic signal to the Specials. Tally pretends she has hidden the locket on the roof of the trading post and heads there with a Special, whom she tricks into letting her climb onto the roof. Through some complicated maneuvering, Tally is able to escape on a hoverboard, knocking the Special off the roof. She is chased by hovercrafts, until she disappears into the partially collapsed tunnel in the mountain, where she finds David, hiding.
The two wait in the dark, hoping they will evade capture. During this time, Tally hatches a plan. She cannot bear to tell David that she has unwittingly betrayed the Smoke, because then she will lose him. But she cannot hide the truth forever. If she is able to rescue the Smokies (David’s parents, Shay, and Croy) that the Specials have brought back to her old city, then she will feel a little better about telling him. Though David is initially skeptical of her plan, Tally assures him that she knows where the captives will be taken because she has been to Special Circumstances before. To cover up the real reason why, she tells David that, after her bungee jacket incident, she was found out and brought there. The reason she never told Shay is that they forbid her to say anything. David believes the lie.
The Smoke is decimated and the library burned. In the wreckage, Tally discovers a pile of shoes. She remembers that Croy saw her barefoot and silently thanks him for convincing the captives to leave their shoes behind so that Tally would have something to wear. She goes searching for the Boss, the only other person she knows got away, and finds him dead in the woods. The magazines are hidden nearby. David and Tally go to check if his parents’ house is still standing. It is burnt to the crisp, but there are no human remains inside, which suggests that Az and Maddie have been captured too. David leads Tally to a cave nearby, where his parents have stockpiled emergency supplies, should an invasion ever happen. They gather what they need and set off.
Passing through a desert created by the orchids, David explains to Tally how the Rusty civilization failed. Someone messed with the chemical compound for petroleum and it turned to phosphorous, which ignites when exposed to air. Tally wonders why she never learned this is school. Maybe because the city didn’t want anyone to know.
Ten days later, they have reached the city. Tally and David scout out Special Circumstances, planning a way to get inside. Tally realizes that the only way in is to use bungee jackets to jump down onto the roof from a nearby hill. Out in the ruins, David sees a safety sparkler flare—it is a new group of uglies (An, Sussy, and Dex) looking to get to the Smoke. He and Tally hide out along the uglies’ path home and surprise them. David asks them to help by creating a diversion. They agree.
In the holding pen, Croy tells Tally that the Specials are separating out the captives by city, so they can take them home. His words make Tally realize that she no longer considers the city to be home; now, her home is the Smoke. Later, when she returns to the decimated remains of the Smoke with David, Tally feels wracked by loss. She watches a wolf attack and kill a rabbit. The parallels between her situation and the rabbit’s are not lost on her. Nature, she ruminates, can be a vicious, uncontrollable thing. It is on no one’s side.
On the way to the city, Tally sees her first desert. It has been created by the environment of "biological zero" left in the orchids’ wake. The interference of men has left the land barren and uninhabitable; similarly, the operation has killed individual spirit.
In learning about the phosphorus that wiped out the Rusties, Tally considers why their society would want the real truth behind the end of the Rusties hidden. David offers that it might be because the government doesn’t want to expose their population to the idea that every civilization has a fatal weakness. Such an idea might inspire people to fight back.
A hurricane in the desert impedes Tally and David’s progress. Tally has never seen weather like this before, and takes it as another lesson in how cruel and arbitrary the natural world can be. As she waits for the storm to end, she looks out on the ruins. Now that she has seen the wreckage of other cities, Tally is further embittered by the way this one has been preserved for tourism. It feels to Tally like everything her society does is in service of some kind of exploitation.
Hoverboarding the river is still a joy for Tally. She feels liberated by the air at her back and the exhilaration of adventure, although this one is for real, not like the tricks she played as a kid. Tally reflects on who she has become: not an ugly, a pretty, or a smokie, but her own person. For the first time, not belonging to a particular group is okay with her, because she has gained self-assurance.