Linh Cinder is a teenage girl who, as a result of an accident at a very young age, is now a cyborg. Parts of Cinder's natural body have been replaced with mechanical ones, and she has a computer interface in her brain. Told that she was orphaned by the same accident that injured her, she is taken in by an inventor, Linh Garan. After his death, her stepmother, Adri, treats her cruelly and forces her to work to support the entire family.
Cinder becomes a successful mechanic in the city of New Beijing, 126 years after the end of World War IV. Despite her success, Cinder avoids telling people that she is a cyborg, as cyborgs are treated poorly. The few people who know that she is a cyborg shun her.
Working in her booth at the market, Cinder removes the mechanical foot that her human body has outgrown and waits on her android, Iko, to bring her a new, larger one. While waiting, Cinder is approached by Prince Kai, son of the emperor of the Eastern Commonwealth. He is in disguise, but she recognizes him. He is looking for the legendary mechanic to repair his android Nainsi, which has mysteriously stopped working.
Kai is surprised to learn that the famous mechanic is a teenage girl, and he flirts with her. Cinder is dismayed because she is insecure. She hides her mechanical foot from him and keeps the glove covering her mechanical hand in place.
After Kai leaves Nainsi, a fast acting plague that has been ravaging Earth, letumosis, hits the market. One of the vendors, the baker, comes down with symptoms. Emergency personnel quickly isolate the baker, Chang Sasha, and test anyone who had contact with her.
Since Iko cannot move fast enough to get out of the marketplace and not be trampled, Cinder and Iko hide in the booth until the area clears. Then they sneak home. There she finds Adri and her two stepsisters, Pearl and Peony, being fitted for gowns for Prince Kai's annual ball. Even though all citizens are invited and Cinder is the family's only breadwinner, Adri tells Cinder that she cannot afford a dress for her. As a cyborg, Cinder has no rights and is treated as Adri's personal property.
Kai appears on a TV-like device, a netscreen, and gives a speech about letumosis, the plague that killed his mother and is killing his father. Since everyone who undergoes plague research catches the disease and dies, a cyborg draft program has been put in place for experimentation. Cinder dreads being drafted, but as a cyborg, she will have no choice if she is selected.
Cinder and Iko prepare to go the junkyard to find spare parts for the family's broken hovercraft. Peony, the only family member who is nice to Cinder, asks to go along. At the junkyard, Cinder tells Peony about her meeting with Kai, and Peony tells Cinder that the rumor on the net is that Kai will choose a bride from among the young women he meets at the ball. Cinder thinks this is ridiculous, as Kai is only 18 years old and unlikely to marry for several years. Peony tells her that the other rumor is that Kai is planning to marry Queen Levana, the ruler of the moon.
Generations before, people from Earth colonized the moon and the Lunars, as they are known, have evolved with strange mind-control abilities that they use for deception and greed. Levana is a cruel queen who rules her subjects through fear. It is believed that Levana murdered her own sister, Queen Channary, to obtain the throne and later murdered her 3-year-old niece by burning the child alive in her nursery.
Conspiracy theorists believe that the child was rescued, badly burned but alive, and taken to Earth. Cinder doubts the story of the princess being alive, but shudders at the thought of Kai marrying the evil queen. Unbeknownst to Cinder, Levana has been trying to force peace with the Earth through a royal marriage to Kai.
While looking for hover parts, Cinder finds a pumpkin-colored, gas-powered car. She fantasizes about fixing the car and driving out of New Beijing. Iko and Peony complain that they want to leave, and when Cinder reluctantly agrees, she notices a red spot rimmed with a purple bruise on Peony's collarbone — a certain mark of the plague. As the rash spreads quickly over Peony's body, Cinder does not want to accept the fact that her stepsister is sick and dying, but the computer portion of her brain diagnoses the illness and confirms that no one has ever survived letumosis. Cinder calls the emergency hovercraft. The med-droids (medical androids) arrive, test Cinder and determine she is free of the disease. They take Peony to the quarantine area.
When Cinder returns home, Adri is furious, blaming Cinder for exposing Peony to the virus. She thinks Cinder was exposed to it in the marketplace. Adri volunteers Cinder for plague research, knowing that no one survives the testing. Cinder refuses to go and fights the med-droids to keep them from taking her. The droids stun Cinder with 200 volts of electricity. Her system shuts down.
While Cinder is unconscious, she has another one of her recurring dreams of being burned alive. When Cinder awakens, she is restrained on an exam table. Her body is being examined, and she is injected with the virus. During the examination, Dr. Dmitri Erland, the lead doctor for plague research, notices what appears to be a clip attached to the top of Cinder's spine.
Terrified, Cinder waits for the effects of the plague to start in her body. She is surprised when her restraints are removed and Dr. Erland comes into the room to meet her. She learns from Dr. Erland that she is not only immune to the plague but very valuable to their research. The doctor is very curious about Cinder's accident and asks her several questions about what happened and how she came to be in New Bejing. Cinder asks Dr. Erland if she can come and go as she pleases, be paid for her help and if Peony can have the vaccine, and he agrees.
In the royal palace's research wing, Kai and adviser Konn Torin watch his father through a glass window. He is in quarantine and has only days left to live. Kai is devastated that his father is dying and fearful of becoming emperor. He goes to visit Dr. Erland to see if any progress has been made on a vaccine.
On the way to find the doctor, Kai runs into Sybil Mira, Queen Levana's representative on Earth. As Kai speaks to Mira, he feels her telepathically trying to influence him with positive thoughts of Levana.
Mira expresses her displeasure that the emperor became sick while in discussions with her queen as they talked about securing an alliance between Earth and the Lunars to avoid war. Kai points out that his father has tried to negotiate an alliance for years and that Levana has always declined. When they are away from Mira, Kai tells his adviser that he does not plan to marry Levana because he knows that she would enslave them. Kai also knows that the if the Earthen Union gets into a war with Luna, they would lose.
Kai tells Torin that he has been trying to find out what happened to Princess Selene because if she is found, she would be the true heir to the Lunar throne and could overthrow Levana. Torin is horrified, telling Kai that if Levana found out he was looking for Selene, she would attack Earth.
Back in his office, Dr. Erland performs a chiropractic procedure to disable the clip he saw at the top of Cinder's spine, and she passes out in pain and agony. When she wakes up, Dr. Erland is standing over her. Kai is there, too. Cinder is relieved she is wearing her gloves so Kai can't see her mechanical hand. Kai asks what Cinder is doing at the research facility, and Cinder is surprised when Dr. Erland lies and says she is there to fix a med-droid. Kai believes the lie and flirts with Cinder, who continues to be flustered and awkward around him. While Cinder would like to be immune to Kai's charms, she really likes the prince.
Cinder knows she has to return home to rescue Iko and wait for the right time to escape. At home, she tells Adri that the researchers did not want her, so they sent her back. The two argue. Adri reminds Cinder that she is unwanted and useless. Cinder takes Iko and goes back to work with the intent of fixing Kai's android and salvaging the gasoline car she found in the junkyard.
Cinder visits Peony in the quarantine area to check on her and bring her a blanket to make her more comfortable. Peony's condition has deteriorated quickly. On her way out of the quarantine, Cinder sees the baker from the market, Chang Sasha, who asks Cinder to bring her young son, Sunto, to visit. Chang Sasha dies while speaking to Cinder, and a med-droid comes over and cuts the ID chip out of her wrist.
Cinder goes back to the research wing of the palace where she sees Kai, also on his way to visit Dr. Erland. Cinder learns that Emperor Rikan has died and Queen Levana will be arriving on Earth in an attempt to solidify a marriage alliance between her and Kai. In Dr. Erland's office, Kai asks Cinder to attend the ball as his guest, but she refuses. Cinder knows that if Kai found out that she is a cyborg, he would be repulsed by her. The ball is also being held on the same night Cinder plans to escape with Iko.
Kai leaves, and Cinder asks the doctor if he knows why med-droids are taking ID chips from the dead. The doctor tells her that since it is illegal for Lunars to leave the moon, those who escape buy ID chips so they can start a new life on Earth with a stolen identity. He tells her that most Lunars, including Levana, have the ability to manipulate bioelectric energy, the energy that is created by all living things. They can manipulate it so people feel what the Lunar wants them to feel or see what the Lunar wants them to see. Levana uses a glamour: an illusion of herself that she projects into the mind of others. That is why the queen always wears a veil when being photographed, and she will not allow mirrors in the buildings when she is present. Lunars who are not born with the ability are called shells, and they are immune to glamour.
Cinder tells Dr. Erland that the queen is due to arrive at the palace that same day, and the doctor panics, telling Cinder that she must stay away while Levana is there. When Cinder demands to know why, the doctor reluctantly reveals that Cinder is in fact Lunar, which is why she is immune to the plague. Cinder is shocked and horrified. She was already an outcast as a cyborg. He explains that Cinder is a shell. Queen Levana would recognize her as Lunar, and since it is illegal for Lunars to be on Earth, Levana would have her killed.
Cinder goes back home and works on the car, as well as on Kai's android. While inspecting the android, she finds a Lunar-made communication chip. When she removes it, Nainsi begins to work again. Using the chip, she tries to reach the person who was taking information from the android, but can't. Against Dr. Erland's warnings, she takes the android back to the palace.
While in the courtyard, the queen makes an appearance on the balcony, using her glamour to brainwash an angry crowd. At first, Cinder falls under the spell, but soon her retina display warns her that what she sees is a lie. Levana notices Cinder and knows she is Lunar.
Cinder quickly escapes the palace courtyard, but Levana furiously accuses Kai and the Earthen Union of harboring fugitive Lunars. She tells Kai that if he is incapable of finding the Lunar girl, she will have her own soldiers dispatched to Earth to do it. Kai and Torin tell Levana that after his coronation, he will hunt for her. It takes all of Kai's strength and energy to resist Levana's glamour, but he does. When she produces a vial of the antidote for letumosis, Kai is barely able to control his fury. The Lunars let millions die, including his father, and they had the cure.
Nainsi finds Kai, and he sends another android to find Cinder, who is hiding outside the palace. She tells him about the communication chip, and Kai is dismayed that one of Levana's people may have been getting information about his research into the whereabouts of the missing princess from Nainsi. Kai again asks Cinder to go with him to ball, and she refuses. Just as Kai gets close and Cinder thinks he will kiss her, Cinder feels a searing pain and passes out.
Kai takes Cinder to Dr. Erland and gives Levana's cure to the doctor as well. After the prince leaves, the doctor tells Cinder that he lied to her about being a shell. The device he disabled in her neck was to block her Lunar bioelectric ability. It was installed by her adoptive father, right before he died. Dr. Erland damaged the device when he tampered with it. Now Cinder will slowly be able to fully use her ability. Dr. Erland accidentally reveals that he is Lunar as well.
Cinder receives a communication that Peony is in the final stage of the plague, and Dr. Erland gives her a portion of the cure, making her promise not to come near the palace or Levana again. Cinder returns to Peony, but the plague has advanced too far; Peony dies before getting the antidote. As the med-droids come to take her stepsister's ID chip, Cinder fights them and takes the chip instead, determined that Peony's identity will not be sold. As she is about to leave, she sees Chang Sunto, the baker's young son, on one of the beds. Cinder quickly gives him the antidote and leaves the quarantine area.
Cinder goes home to find Adri furious with her. Her stepmother found out that Cinder bought a new foot and demands it back. Without a foot, Cinder has to use crutches to walk. At her booth on the day of the ball, Kai visits and gives her a pair of beautiful silk gloves. Again, she refuses to attend with him, even after Kai admits that he has feelings for her. Cinder's stepsister Pearl sees the gloves. In a fit of jealousy, she dumps them on the dirty ground.
When Cinder is alone in the apartment that night, she packs the few things that she has in preparation to leave. She finds the old cyborg foot that she thought had been thrown away. As she prepares to cut the ID chip out of her wrist, the communication chip she took out of Nainsi begins to work.
A Lunar girl, a programmer, contacts Cinder and tells her that Levana had the communication device installed in Nainsi. Levana knows that Kai is looking for Princess Selene with the intent of having the queen deposed. Feeling guilty for helping the queen and as a prisoner to Levana herself, the girl wants to get a message to Kai: Levana has no intention of abiding by the treaty. Once they are married, she will kill him, take over the Commonwealth and wage war on the entire planet.
Cinder believes that Kai will announce an engagement to Levana at the ball. She wants to contact Kai but knows he will not check his messages during the event. She attaches the old foot, puts on Peony's crumpled ball gown and the dirty silk gloves and heads to the ball in the old orange car. Cinder rushes to the ball, but a sudden rainstorm causes her to crash the car. She has to walk the rest of the way to the palace, soaking wet. She realizes that her plan to escape New Beijing is gone.
Cinder tries to enter the ball unnoticed, but as a guest of the prince, she is loudly announced. Everybody's attention turns to her, and Cinder is embarrassed about her appearance; but she is determined to warn Kai. Instead of being angry, Kai dances with her. Cinder uses the opportunity to tell Kai about Levana's plans. Despite her warnings, Kai decides to go forward with the marriage to avoid war and get the cure for the plague. While the cure healed Sunto, it cannot be replicated, and he needs to get it directly from the Lunars. Desperate, Cinder kisses Kai in front of everyone, including Levana, and announces that Kai is already in love with her.
Levana laughs at Cinder, making it clear that she doesn't care if Kai loves someone else. She just wants to be empress. She tells Cinder she wants her dead and asks Kai if he is ready to bargain for Cinder's life. Kai tells Levana that he cannot have peace at the expense of freedom, so he cannot marry her.
Levana is furious, and Cinder is surprised to realize that she can see through the queen's glamour. Levana uses her ability to force Cinder to grab a gun to shoot herself. The intensity of the situation causes Cinder's bioelectricity to spike, causing fireworks in the ballroom. Levana has a moment of shock when she realizes who Cinder truly is. Cinder fights the compulsion, tries to shoot Levana but shoots a Lunar guard in the shoulder instead. She drops the gun and tries to escape, but her too small cyborg foot falls off, leaving her incapacitated.
Kai, seeing that she is both a cyborg and Lunar, asks Cinder if she used her ability to manipulate him. He tells Levana that he will turn Cinder over to her on the condition that she doesn't start a war with Earth. Levana agrees. While Cinder is sad that Kai feels deceived, she knows that he is making the right decision for his people and accepts that Levana will kill her as soon as they are back on Luna.
Cinder is taken to a prison cell where Dr. Erland visits to give her a new, enhanced cyborg hand and foot that will help escape the holding cell. He also tells her that her blood tests prove that she is Princess Selene of Luna, and their only hope of overthrowing Levana. Cinder is shocked and realizes that Levana recognized her. Dr. Erland urges her to escape and meet him in Africa where he will continue his plague research. At first Cinder considers the impossible task of escape, and then she wonders what will happen to Kai if she gives up and allows Levana to kill her. She strengthens her resolve, cuts her ID chip out of her wrist and plans her escape.