Jack is sitting at the table with his parents and planning an escape in his head. He has a flashback memory from past when he became Jack, a boy, and left life as a girl, Jacqui, behind. Jack is actually a girl pretending to be a boy, because of the dangers of being a woman in this destroyed world, dangers like raiders, who rule the world outside of the wall and take every woman that comes their way.
The world is destroyed after all the bees are gone, and those who took injections to fight the bee flu mutated to beasts, raiders or fecs; beasts being the most dangerous form of mutation. Those inside the wall are safe and live a fairly normal life, while those not so fortunate who are left outside, find a way to survive on their own. Such is Jack's family, who've managed to keep Jack and her mother safe by transforming their appearance and manners to seem as male.
One of Jack's brothers, Dean, is missing, and she decided to escape home to go look for him. She runs to the wall to find her friend from her old life, Fiona, to ask her about Dean, because he left home to bring Fiona's mother to safety and then never returned. Fiona comes out with Bowen, they are a couple and with Jonah, her brother, whose body is covered with scars. They agree to go with her to search for both Fiona's mother and Dean.
On their way, they come across a man called Flint, who gives them a map marked with a path to Wyoming, which is supposed to be a safe place. Jack suddenly remembers Flint as a raider who once came to her home looking for her father, who is a dentist. They manage to escape before the raiders come to take them, but while they run, Jack is split from the rest of them. She is suddenly caught by a vagabond, who occasionally came to her home in search for food, and he helps her escape the raiders and advises her to keep of the path, so that they can't track them.
Jack reunites with the rest of the group, and they search for shelter. Jack reveals that going to Wyoming is not a good idea, because she remembers the time when one of her father's raider patients revealed that Wyoming is a trap set by the raiders. They also talk about sirens, people who are supposed to be tricking and leading people to raiders.
In the middle of the night Jack hears Jonah fighting with someone, who turns out to be a little beast boy. They restrain him and go find shelter in an abandoned house. There Fiona reveals that there is a cure for beasts, and that they are carrying it with them. She injects it into the boy.
Jack goes out to keep watch. She suddenly sees a shadow of someone not far away from her. Scared and confused, she turns on the flashlight, and sees the figure running towards her. She fights and cuts the person, but he tries to calm her down, saying that he only wanted to turn off the flashlight because of the raiders. He tries to convince her that he is not a danger to them. His name is Kevin, and he warns her that they have to leave their hiding place, because raiders will find them soon.
They run back to the shelter to warn the rest of the group. Since Jack is the fastest runner, she is to serve as a decoy while the rest escape. While she runs, she notices someone catching up to her, it is Kevin. They run into the raiders and Jack hides while Kevin distracts the raiders. They manage to escape on a four-wheeler together.
Kevin takes Jack to his underground shelter, which is pretty much a small apartment underneath the earth. After they get some rest, Kevin decides to go look for Fiona, Bowen and Jonah together with the beast boy, to bring them to safety as well. He convinces Jack to stay behind.
While Kevin is away, Jack discovers a secret door that leads to a storage packed with food and a house below. In one of the rooms she discovers a telescope and with it she catches Kevin leading the group towards the shelter. She quickly returns to the shelter, before they arrive there first.
The group rests and eats and Kevin and Jack are left alone in the kitchen where he confesses to her that he knows that she is not a twelve-year old boy, but a sixteen-year old girl. They share a kiss, which doesn't leave either of them indifferent.
Bowen asks about the big bag they gave to Kevin to carry, but they left it behind while escaping the raiders. Bowen and Fiona are upset because that bag contained the cure and the formula for the cure. They have to get that bag back, which means they have to go straight to the raiders' nest for it. They make a plan for retrieving it and the boys set out on that mission, while Fiona, Jack and the beast boy, who is in the recovering phase, are left at the shelter.
Fiona is sick with worry and Jack decides to reveal the secret passage to her. There Jack discovers dirt-filled clothes and other disguises for a vagabond, she discovers two letters, AB, made with metal string, which is one of Kevin's hobbies. She pulls out the letter J she's always carrying with her, made in the same way. It is a gift, the vagabond who often visited her home gave her in exchange for her kindness. Kevin is that vagabond. They go to the room with telescope and discover the boys unknowingly heading straight into a group of raiders. Jack decides to run to them to warn them before it's too late. She arrives to find only Kevin. Kevin turns against her and hands her to the raiders, he confesses to being one himself, but he doesn't reveal the fact that she is a girl. He already handed them Bowen and Jonah.
Jack is taken to the raiders' nest, and she sees Bowen and Jonah tied up. The raiders have planned to use her for the neck-tearing practice. Being taken to a cell, Jack vomits and faint and wakes up during a night, in a cell together with Jonah. Jonah helps her heal, one of the side effects of being a cured beast is the healing ability, and tells her that Kevin is not a bad guy and that he had no other choice but to hand her to the raiders.
After Jonah is taken away, Kevin comes to Jack's cell and tells her to follow him; he will help her escape and explains what neck-tearing practice means. It is a test of virus-injected dogs that are released on the human victim to tear their necks, to see how efficiently they kill humans. He leads her out of the building and pushes her to run. Jack runs as fast as she can, but she is hindered by her injuries, and is soon caught again and led back to the raiders.
The raiders take her to one of the leaders, Soneschen, who was previously in charge of the wall and refused to take Jack's entire family in, her and her mother to be precise under the excuse of them being overweight. He makes her recall the Solomon story from the Bible, a story of a mother's sacrifice, which mimics Jack's mother's intent to sacrifice herself in exchange for her daughter to be able to live inside of the wall. It means that Soneschen remembers her from that day, which means he knows that she is female. He commands for her to be tied to the tree outside, to make the one who helped her escape come out.
Outside, the leader of the raiders, Hastings, makes an appearance to discuss her fate. Hastings is none other than Jack's brother, Dean. He asks if someone wants to take Jack's place, to die instead of her and Kevin volunteers. He is tied to the tree and Jack is taken inside. She watches how Dean releases dogs onto him, pulling them back just before they reach him, to give him a taste of his fate the upcoming day.
Jack and Kevin are put in the same cell, and Jack, realizing that she won't be able to live with herself if Kevin sacrifices himself for her, decides that she will face death instead. In the middle of the night, Jonah and one of the old raiders, a man called Zeke, come to the cell and Jonah punches Kevin to make him unconscious and to take his place, because his beast strength makes him more likely to fight off the dogs and protect Jack-Soneschen decided to bring both of them to the neck-tearing after all.
The day of Jack's death sentence arrives, and she and Jonah are taken to the playground surrounded by raiders eager to watch the show. Dean, Soneschen and Flint are at the center and Dean gives a speech about his experiment on the dogs-they only respond to his voice, they only attack men, and he plans to release them into the wall to kill off the men and leave women for the raiders.
Before he releases the three dogs, Jonah tells Jack to try to not kill the animals; he reveals the syringes with cure that he plans to use on the dogs. One of the dogs jumps at her and bites her arm, but then stops attacking her. Jonah injected the two dogs, and gives the last syringe to Jack to use it on the remaining one. Then he lets himself be pushed down by the animals.
Dean suddenly calls off the dogs and pushes Soneschen and Flint towards them and reveals his true plan-to release the remaining modified dogs onto the raiders to destroy them. He helps Jack and Jonah escape together with Zeke and Kevin and returns to the released bloodbath. Kevin tells Zeke to take Jonah and Bowen to the shelter, while he takes Jack somewhere to help close her wound.
Kevin and Jack are intercepted by Soneschen, and he gets on top of Kevin trying to choke him. Jack takes her father's gun and kills him. They go back to the shelter and reunite with rest. After a while Jack is reunited with Dean as well.
They all pack up and set out to the safe place in the mountains, a blooming place where bees aren't extinct. They arrive there and Jonah and Fiona are finally reunited with their mother, Dean is reunited with his wife and child and Kevin with his grandfather and beast sister, who is finally going to be cured.
