Crescent Moon, or Cress, as she is called, is a 16-year-old Lunar girl who has been imprisoned in a satellite station for most of her life. Cress was born without bioelectric Lunar ability and is considered to be a "shell" by her people. All shell babies are taken away from their parents to be killed, but they are actually secretly kept alive and their blood is used for experiments. Cress proved that she was adept with technology at a young age, so Queen Levana's head Thaumatuge, Sybil Mira, locked her in a satellite orbiting Earth. There, she serves as Levana's programmer and hacker, spying on Earth's heads of state.
In previous novels, Cress sent messages through Emperor Kai's android, warning him that Levana intended to marry Kai only to become empress and then kill him. The message was discovered by Cinder, a cybernetic teenage girl, who later found out that she is the orphaned princess of Luna, Levana's niece and the true heir to the throne. In order to secure the crown, Levana tried to kill Cinder when she was a toddler by setting fire to her nursery. Unbeknownst to Levana, Cinder survived the assassination attempt and was smuggled to Earth by Lunars who wish to overthrow the queen. As a result of this fire, parts of Cinder's body were severely injured and had to be replaced with cybernetic parts.
Cinder was arrested for trying to kill Levana, but Dr. Dimitri Erland, the leading researcher for the letumosis plague, gives Cinder tools to help her escape, telling her to find him in Africa after she breaks out. Dr. Erland is secretly a Lunar living on Earth. He had a shell daughter, Cresent Moon, who was taken away according to lunar law. He believes she is dead. Dr. Erland escaped his world and has worked to find the true Lunar heir, who he hopes will depose Levana.
Cinder and another prisoner, Carswell Thorne, escape and retrieve Thorne's stolen ship, the Rampion. Through technology, Cress helps Cinder and Thorne evade the authorities. Dr. Erland asks Cinder to meet him in Africa, but first, she goes in search of an Earthen woman and another Lunar scientist who helped her escape from Luna as a toddler. She finds out they have both died. After helping the woman's granddaughter, Scarlet Benoit, and a Lunar operative, Wolf, escape from the Lunars, Cinder decides to find Cress in order to uncover Levana's secrets.
Cinder and her crew (Scarlet, Wolf and Thorne) contact Cress and agree to rescue her from her satellite prison. Cress packs up her meager belongings and prepares for rescue, but an unexpected visit from Sybil Mira turns dangerous. Cress is shy, socially awkward and has extremely long, blond hair. It has never been cut. She also has followed Thorne's career of civil disobedience from a distance for years and has a crush on him.
Mira discovers Cress' intentions and sets a trap for Cinder and her crew. The trap results in Scarlet being captured, Wolf being shot and Thorne and Cress being trapped in the satellite as it falls toward Earth. During the ambush, Cinder manages to use her Lunar mind control gift on Mira's pilot, Jacin Clay, forcing Clay to help her fight off Mira. Afterward, Clay tells Cinder that he is faithful to Lunar's one true ruler, and he will help her regain her throne. Cinder is skeptical, but needs all the help she can get.
The crew is now separated, with Cinder not knowing if Thorne and Scarlet are dead or alive. With Wolf unconscious and dying from his gunshot wound, Cinder makes the decision to meet with Dr. Erland in Africa to get his help. Dr. Erland is continuing his plague research in a small village in Africa, using blood from a colony of Lunars that have been secretly living there. Immigration from Luna is illegal, so the people who do escape live on Earth in secret. The Lukemosis virus has been killing Earthens for more than a decade, but Dr. Erland reveals to Cinder that there is a mutated version of the disease that can kill Lunars as well.
Cinder lands in the small desert town of Farafrah in North Africa and meets Dr. Erland. The doctor tends to Wolf's wounds, while the people in the town, most of them fugitive Lunars, bring Cinder gifts and tell her how much hope they have that she will overthrow Levana.
Cress and Thorne survive the satellite's crash landing in the Sahara Desert, but Thorne hits his head during the fall and is now blind. He has to rely on Cress to direct them through the desert with the meager resources they scrape together from the satellite. Cress cuts off her hair and fashions shoes out of cloth. She has lived so long in the confines of the satellite so it isn't long before she begins to get severe blisters on her feet. Additionally, both Cress and Thorne suffer horribly from sunburn, heat exhaustion, starvation and dehydration. Near death, they are found by a group of travelers who sell wares from town to town. Thorne lies to the group, telling them that he and Cress are newly married and were robbed while on their honeymoon. Thorne is still a fugitive, and he knows the authorities must have found the crashed Lunar satellite by now.
News of the satellite spreads, and the travelers, who turn out to be Lunar traffickers, deduce that Cress is Lunar. They kidnap Cress and sell her to Dr. Erland, who is known in the area to buy Lunar subjects for his experiments. When the kidnappers sell Cress to Dr. Erland, he is struck by how much she looks like his wife. Before he pays for her, he draws her blood. He believes his daughter was killed by Levana's order, but he holds out hope that this is her, and the tests confirm that he is her father. He holds on to the information, with plans to talk with her in the future. Thorne follows Cress, determined to rescue her.
Before long, Cress, Thorne, Wolf and Cinder are reunited. Cinder sees a news feeds that Thorne has been spotted. They prepare to leave town together, but the authorities find them. With the help of the Lunar townspeople, who use their bioelectric gift, the group escapes.
Aboard the Rampion, Cinder hatches an elaborate plan to infiltrate the castle and kidnap the groom, Emperor Kai, to stop the wedding. She knows this act will start a war, but she plans to take the crew to Luna, reveal that she is Princess Selene and rally the Lunars to dethrone Levana.
Using stolen invitations, Cress and Wolf attend the wedding as guests. Wolf incapacitates the guards while Cress deactivates all the palace security systems. Dr. Erland and Thorne sneak into the palace's medical wing. There, Dr. Erland works to cure Thorne's blindness, as well as raise the plague alarm and provide a distraction for Cinder.
While in the labs, Dr. Erland sees the first signs of the mutated form of the plague in himself, so he leaves a video message for Cress and quarantines himself. Cinder goes to Kai's private quarters and tries to convince him to go with her, but when he won't because of his responsibilities as a ruler, she shoots him with a tranquilizer dart and kidnaps him.
The group meets at the medical lab where a quarantined Dr. Erland tells Cress (through portioned glass) that he is her father, he never wanted to abandon her, and he has always loved her. They are forced to leave him to die. Just before they are to get in the waiting escape pod, they realize their pilot, Clay, has been taken. Mira now has control of their ship. The group fights with the Lunar soldiers, but the main battle is between Cinder and Mira. Cinder succeeds in breaking Mira's mind, driving her insane. This leads Mira to jump off the palace roof to her death.
Levana goes to the quarantined area of the lab to see Dr. Erland. He tells the queen that instead of killing shells, her researchers have used their blood to create the plague for biological warfare. The Lunars, who escaped to Earth, unknowingly brought the plague with them, as was Levana's plan. The cure can only be made using the blood of shells. Dr. Erland dies after telling Levana that Cinder is the true heir to the Lunar throne and will overthrow the queen.
Safely aboard the Rampion, Thorne tells Cress that his crimes were not heroic or noble, but were actually selfish, self-serving acts on his part. He is afraid that now she really knows him, she will think differently of him. Cress does not admit it, but she in more in love with Thorne than ever before.
Kai wakes up and is furious to find himself in orbit aboard the Rampion. He confronts Cinder with his fear that this will start a war. Cinder tells him that war is inevitable; marrying Levana would never have stopped it. Kai admits that it was a bad decision, but he had no other choice. Cinder asks him to join with her to stop Levana's rule.
She reveals that she is Princess Selene. At first Kai is shocked, but then he realizes that this is why Levana put so much time, effort and resources into catching and killing Cinder.
He asks Cinder if she ever used mind control on him, and she tells him she never did and never will. They kiss but stop when Cinder sees a news feed that Levana's armies have massacred all the people, both Lunars and Earthens alike, in Farafrah.
Cinder is heartbroken and feels responsible for the deaths of innocent people, whose only fault was that they helped her escape. Cinder also admits to Kai that she is scared of Levana and of peoples' expectations of her to be their princess. She is also fearful that using her power makes her a lot like Levana. Kai assures her that she is not like Levana and tells her that Lunars don't need another princess; they need a revolution. The couple get word that Luna has attacked all the countries on Earth. Cinder tells Kai she is going to Luna to start a revolution.