In the kingdom of Goredd, dragons and humans are preparing to celebrate the 40th anniversary of the signing of the truce agreement between the two species. Since then, dragons have been allowed to take on human form and live among the people of Goredd, attending and teaching school, working various jobs, learning the ways of human beings, but strictly forbidden to fully immerse themselves as human.
Seraphina is a young woman who works as the assistant to the court composer. She also hides a dangerous secret: She is half dragon. Her mother, a dragon from a prominent family, fell in love with a man while in her human form. Her deceit was discovered when she died giving birth to Seraphina. Her father kept the truth hidden until Seraphina developed silver dragon scales around her waist and arm when she was 11. She promised not to bring notice to herself, because to be half dragon is considered an abomination by both species.
However, when she must play her flute at the funeral of Prince Rufus, the heir to Goredd’s throne, everyone marvels at her musical talent. After the service, Seraphina meets with Orma, her tutor and uncle, who is a full-blood dragon disguised as a human. A street urchin gives him a gold coin, which, Seraphina notices, causes him distress. Before she can ask about it, a new skin — a dragon who is new to human form, comes under attack from an anti-dragon group.
Prince Lucian Kiggs, bastard prince of the realm and captain of the guard, arrives to break up the fight. He recognizes Seraphina from the court as she instructs his cousin, Princess Glisselda, in music. She and Orma leave before he can question them in depth.
Seraphina returns to her duties at court, tutoring Glisselda and arranging the entertainment program for an upcoming celebration. One night as she walks to Orma’s house, she sees a quigutl, a smaller species of dragon who cannot don human form. Feeling sorry for it, Seraphina gives it money for a tiny figure of a lizard with a human head.
After they trade, two men chase the quig off, and Seraphina pretends to have been offended by its panhandling. Before the men can help her home, she is struck by one of her debilitating visions. The visions, which always show one of several humans with odd features, come on fast and strong.
Orma has taught her how to “tend to” these oddities, as if they were plants in a garden. She daily visits them and makes sure each one remains in its prescribed place in her mind, but sometimes one will force her to have a vision. As she falls unconscious, she sees the boy she has named Fruit Bat, because he often hangs upside down in trees and eats fruit. For the first time, he appears to see her. When she wakes up, one of the men tells her he found the quig figure in her purse. He tells her to repent or be wary of the consequences.
The following evening, Seraphina attends a dance at court. Josef, the Earl of Apsig, holds several women’s attention when he tells the story of how Prince Rufus was killed by a dragon while hunting. Seraphina tries to convince him that someone other than a dragon may be the murderer, but Josef belittles her. She is shocked to see one of the people from her visions at the dance.
Later, she visits the woman in her mind and is pulled into another vision. She sees the woman, whom she has labeled Mrs. Fusspots, undressing in a room of the palace. The woman has a stubby tail covered in dragon scales, and Seraphina realizes she must be another half-breed. The woman senses Seraphina’s presence and tracks her down using her heightened intuition.
She is Dame Okra Carmine, and she swears Seraphina to secrecy. Seraphina realizes that the other odd people in her visions must also be half dragons. Over the next few days, she meets Fruit Bat, who is actually a young dancer named Abdo, and Loud Lad, who is really Lars, the bastard brother of Josef. She learns that she can communicate with them telepathically.
Orma finally admits that the coin he received was a message from his father, Imlann. The ancient dragon sent it as a warning that Orma must not reveal his presence in Goredd. Seraphina knows that Prince Lucian, who is investigating the death of Prince Rufus, must be warned that Imlann may be plotting to assassinate Ardmagar Comonot, the leader of the dragons, when he visits for the upcoming celebration.
Seraphina learns from Glisselda that two banished knights, former dragon hunters, claim to have spotted a rogue dragon in the countryside. Seraphina pretends to be assisting Prince Lucian in the investigation of Prince Rufus’ death and visits the knights in jail. They describe the dragon they saw, and she hopes it will be enough for Orma to identify it as his father.
Prince Lucian arrives, suspicious of her motives until she tells him about Orma, although she leaves out the part about him being her uncle. Prince Lucian suggests they join forces in the investigation. Seraphina agrees. She and Orma discuss the developments but come to no conclusion. Orma gives her one of his tracking earrings so that she may call to him for help, should Imlann attack her. The following day, Prince Lucian arranges to ride out with her to the country and interview another knight who may be able to positively identify the rogue dragon.
Lucian and Seraphina interview the knight and learn, to the best of his recollection, the dragon he saw was indeed Imlann. As they make their way back to the city, Imlann blocks their path. He can smell the dragon scales on Seraphina and so believes she is a dragon in disguise. She uses Orma’s earring to send him a distress signal, then bluffs Imlann into believing she has a device implanted within her that will explode should he attack.
He flies off with the warning that he will return soon for battle. Seraphina convinces Lucian that she is not really a dragon, nor does she have any dragon devices on her. Unfortunately, as they embrace in relief, Orma appears in dragon form in answer to her call. Lucian is furious to have caught her in a lie. He also believes she is illegally working with the dragons. He orders their arrest. Seraphina wonders how Imlann knew their location. She suspects Josef may be a spy. Still angry that she lied to him, Lucian refuses to discuss the possibility.
The Queen and the visiting Ardmagar question Seraphina and Orma. All their transgressions are forgiven as they were working to keep the peace. Orma asks to speak to the Ardmagar with only Seraphina present. He asks to be excused from constant scrutiny by the Censors who monitor dragons, looking for signs that they are becoming too human. Seraphina, in an effort to help his cause, admits that he is her uncle.
The Ardmagar becomes enraged. He revokes Orma’s teaching license and orders him to have his brain excised, a process that will remove all his memories. Later, Orma confesses to Seraphina that he will never subject himself to the procedure. He will live in hidden exile until she needs his help. That night, she has a vision caused by an implanted memory from her mother. It reveals how Imlann, her grandfather, plans to overthrow the Ardmagar and destroy the peace between dragons and humans.
On the final night of the Ardmagar’s visit, Seraphina and her friends Lars, Dame Okra and Abdo keep watch over him during a ball. They realize too late that the royal family is also a target for the assassin. Glisselda’s mother is found in her room, having just drunk poisoned wine. Seraphina enlists Dame Okra and her heightened intuition to find Glisselda, her grandmother, Josef and Lady Corongi, Glisselda’s tutor.
They interrupt the group as they are about to share a toast. Lucian and Seraphina accuse Josef of treachery, but he pleads his innocence, pointing his finger at Lady Corongi. The quig figurine of the lizard man utters the truth. It is a tool that can spot dragons in disguise. It calls out Lady Corongi. She flees the room with Glisselda over her shoulder, transforming into Imlann.
Seraphina tries to distract Imlann by telling him the truth of her identity. She gains enough time for Lars and Abdo to find them. Abdo climbs on Imlann’s back, and Lucian is able to stab the dragon’s feet to release Glisselda. Imlann takes off with Abdo, but is stopped in the air by Orma. Orma purposely does not go on the offensive so that Abdo will not be harmed.
After battling, Orma crashes to the ground while Imlann escapes. Other dragons that support the peace treaty stop him. Seraphina is relieved to find that Abdo survived by jumping onto Orma’s back in the air and that her uncle is severely wounded, but alive.
The following day, Glisselda, as acting queen, gathers the representatives of other human kingdoms to gain their aid in the coming war with the dragons. She also convinces the Ardmagar to find younger dragons to fight to maintain the peace against the older dragons that wish it destroyed. Finally, she enlists Seraphina to locate the other half-dragons to see if they will side with Goredd in the coming war. After the meeting, Seraphina visits Orma. He is recovering, but will soon go into hiding so that he will not have to be excised. Seraphina and Lucian admit their mutual love for each other, but as he is betrothed to Glisselda, they agree they will not act on their feelings. They hope that after the war, Glisselda may release him from his promise, but until then, they will serve her and the country, and remain only friends.