Picket Longtreader is a young rabbit, who has risen to fame because of his heroic effort to save Prince Smalls, the heir to the throne of King Jupiter. The two rabbits begin the novel on a mission to free Picket’s parents and younger brother from a slave camp. Unfortunately, the information they received was faulty and the slaves have long been moved to a new, unknown location. Enemy birds attack them, and they only escape death when other soldiers from their warren rescue them.
Picket’s older sister, Heather, has become a doctor in training. Although she enjoys the work, and has found some fame herself because of her storytelling, she is unhappy. She has been experiencing nightmares and is worried about her family.
After venting her worries to her best friend and mentor, Emma, Heather meets with Lord Ramnor, the head of their warren, to receive her assignment as a trained apprentice. Although she thought she would be Emma’s assistant, Ramnor assigns her to be the field medic to the Fowlers’, an elite rabbit squad that includes her brother.
Heather is heartbroken that she must replace Heyward, who was a gardener before Morbin attacked their old warren. Heyward leaves the Fowlers a dejected rabbit. Heather tries to console him, but he is frustrated because he does not know where he fits now that war has arrived.
Smalls interrupts Heather’s pensive thoughts and tells her of his coming meeting with the other rabbit lords who refuse to recognize him as the future king. He asks her to come to a private meeting in Lord Ramnor’s room that night. News arrives that an army of rabbits is marching from the southwest. No one knows if they are friends or foes.
Picket and Heather counsel the prince to go to the conference and not stay behind to fight. The uniting of the remaining rabbit citadels is too important to put off. Smalls agrees, but only if Heather and Picket promise to protect the secret heir to the throne, his sister, Emma. She has no idea that she is a princess, and Smalls does not want her to know, as her ignorance could save her life.
Before he leaves, Smalls confides in Picket that new information has come about where Picket’s brother and father may be held. As it is close by, Picket wants permission to take the Fowlers there to try and free them, but Smalls has been advised that the squad must stay to protect the warren from danger. Frustrated, Picket begs Smalls to continue the search when he makes his diplomatic journey and the prince agrees.
The following day, wolves attack the warren. Heather and Picket protect Emma, although she does a good job of defending herself. Once Emma is safe, Picket returns to the battle, and Heather searches for Lord Ramnor. She finds the lord mortally wounded in his room.
As the warren looks to be overrun, there is a great shout and a symphony of horns. The large rabbit army that was headed in their direction arrives and defeats the wolf army. The new army is from Terralain and is ruled by King Bleston, the older brother of King Jupiter. His son Kylen, called Kyle, was Heather’s friend and the one who betrayed Smalls to Morbin and nearly got the prince killed.
Heather and Picket try to make sense of the new order in the warren in the days after the battle. King Bleston begins to take over command of the rabbits, calling for meetings and such. Heather is surprised to see her old friend, Heyward, dressed in a religious robe. He was inspired by the peace he saw in a brother’s eyes during the battle and decided to join the order so he could experience it.
Heather and Picket are summoned to a meeting with King Bleston. They speak with Kyle in his father’s room. Kyle asks them to forgive his betrayal of Smalls, but Heather and Picket cannot. Kyle urges them to listen to what his father, King Bleston, has to say.
Bleston calls Picket and Heather royalty and says that all rabbits in Terralain are free and noble, if they accept it. He considers himself the king who makes other kings. Bleston wears the Whitson Stone, the emblem of the rightful ruler. Both Heather and Picket worry about what Bleston will do when Smalls returns. Bleston asks them to accept his rule while Smalls is away. When the prince returns, they will negotiate how to rule the new world together.
King Bleston soon takes over rule in the secret citadel. Many appreciate his firm hand and military prowess, but Heather still has her doubts. They are amplified when elderly healer Aunt Jone is imprisoned for taking supplies from Bleston, something Lord Ramnor never minded. Heather retrieves the old rabbit’s new remedy as soldiers take her to jail. Although she carries it with her constantly, she forgets she has it.
Picket considers sneaking out of the citadel to find the news from the other warrens. He is commanded to go to Bleston’s rooms for an audience. Picket is afraid Bleston has uncovered his plan, but instead the king urges Picket to follow his heart and lead a rescue attempt for his family.
Kyle, now known as Prince Kylen, approaches Heather and asks her to speak with his father. He counsels her to present her opinions to him, but to allow the king to share his as well. On the way to the meeting, a wolf attacks them. Kylen is injured in the attack but manages to save Heather’s life.
Later, as she tends his wounds, King Bleston arrives and speaks with her. They talk honestly about the decisions to be made. Bleston does not want to rule for himself, but to leave the kingdom to Kylen. Heather encourages Bleston to be a true kingmaker and put Smalls on the throne, thus incurring the love and respect of rabbits everywhere. In an announcement before the entire warren, King Bleston promises to do just that when Smalls returns.
The rabbits make plans to attack Morbin’s army. They will be horribly outnumbered, but they hope the action will spark their road to freedom. A warning blast comes from the perimeter, so Picket and the Fowlers investigate. They find Picket’s Uncle Wilfred wounded.
He brings terrible news. Smalls is dead. Uncle Wilfred counsels Picket not to take on the guilt of the prince’s death, even though he died trying to free Picket’s family. Emma is told her true identity, and she vows to fight for the Mended Woods, just as her brother would have done.
Morbin’s soldiers outnumber Picket and the rabbit army. Nevertheless, the rabbits fight bravely, luring the wolves into a trap that allows the rabbits to use their catapults. The final piece of the plan was to have King Bleston’s army attack the wolves’ rear flank so Picket and the Cloud Mountain army could then escape.
But King Bleston never arrives, leaving the rabbit army to be slaughtered, as birds of prey arrive to help the wolves. Picket and the Fowlers run to the front of the line and inspire the rabbit army to fight to the death. Heyward pulls Picket aside to show him an invention he has made. It is a type of hang glider that will allow Picket to fight the birds in the air. Heyward uses a catapult to launch Picket, and he begins his aerial attack.
Meanwhile, King Bleston betrays Emma. He has made a deal to bring her to Morbin in exchange for his own kingdom and a treaty of peace. He will kill Heather unless Emma agrees to willingly go to the bird king’s lair with Garten Longtreader, Heather’s traitorous uncle.
Lord Rake, Emma’s adopted father, is killed trying to protect her. Picket drops from the sky to fight against King Bleston. The two rabbits plunge over a cliff. King Bleston dies. Garten agrees to take Emma back to Morbin, where he will negotiate for Kylen’s reign. If Garten does not blow a signal within the hour, signaling a carrier to come and deliver him safely back to Morbin, then another wolf army will attack Cloud Mountain and kill them all.
Picket flies back to the plateau, ready to fight Garten and anyone else who tries to harm Emma, but she insists on speaking with Garten alone. Picket sends the rest of the rabbit army to save his friends who are still battling on the plains below. Against Picket’s and her army’s wishes, Emma commands that Garten be allowed to return to Morbin unharmed. As the day ends, the beleaguered rabbit army returns, their numbers severely diminished, but they have survived to fight again.
Heather wakes in the middle of the night and knows she must find Emma. She finds her friend ready to use Garten’s whistle to call one of Morbin’s birds to take her to the bird king. Emma had made a deal to sacrifice herself for her people. Before the bird arrives, Heather pushes her friend down and takes her place.
As Heather stands before Morbin, he calls Garten forward to verify she is indeed the princess. Garten confesses that she is his niece. Morbin calls for his forces to attack and destroy Cloud Mountain for Emma’s defiance, but leaves no orders concerning Heather’s fate. As she struggles to stay strong, a song rises from somewhere among Morbin’s rabbit slaves. It is an ancient song of victory. More than that, Heather recognizes the voice of the rabbit singing and her heart is filled with hope.