Prologue
The book began four years before the events of Moon Rising with Moonwatcher's mother, Secretkeeper, who had hidden Moon's egg in the rainforest to keep it safe. She frantically traveled from the NightWing island to get to Moonwatcher before her egg hatched alone. On the way there, she was held up by Farsight and Preyhunter, but managed to excuse herself in time. Not finding her egg immediately, she had sudden doubts and questioned why she ever thought it was a good idea to lie to the tribe. She did not trust the father, who was confirmed to be Morrowseer, and kept it secret from him. Moonwatcher hatched from a silver egg under two full moons and got her name when she tilted her head up to look at the moons. Some time after, Preyhunter called her, but Moonwatcher had to stay hidden. Secretkeeper realized that Moonwatcher could read minds, though she did not believe the old legends at first.
Part 1: Welcome to Jade Mountain
Moonwatcher was very nervous about going to school. She thought everyone would do something bad to her and hate her if she revealed her powers. Secretkeeper, who was there, spotted three SeaWings, who Moon identifies as Queen Coral with two of her daughters, Anemone and Auklet. Tsunami, greeting them, beamed in delight when seeing Anemone and another SeaWing, Turtle, who was one of Tsunami's thirty-two brothers. Tsunami appeared to be shocked at the fact that she had that many brothers. Anemone was put in the Silver Winglet, and Turtle was put in the Jade Winglet with Moonwatcher. Then Coral left with Auklet, followed by Secretkeeper. Moon went into Jade Mountain Academy, where Fatespeaker greeted her excitedly, commenting on Moon's teardrop eyes scales and how shiny and big they were compared to hers, then asked Moon her name. She repeated the the NightWing's nickname as she looked for Moon's cave on a scroll. She found it, exclaiming, "You're going to love your clawmates." As Moon went to find her cave, she read several minds and wondered how she would cope with other dragon's thoughts constantly bombarding her. She then noticed a scroll rack on the wall and one by the door. The sign above the one above the door said, Free reading! Hope you like them.In her cave, she heard a voice in her mind, who is later revealed to be Darkstalker. Moon shared a cave with Carnelian, a grumpy SkyWing, and a RainWing named Kinkajou who she quickly became friends with. They were both in her winglet, the Jade Winglet, along with Turtle, his clawmate, Umber, a SandWing named Qibli, and an IceWing named Winter. Later, in the library, Moon borrows the scroll The Animus Historiesfrom Starflight and finds out that the mystery voice is Darkstalker.
Part 2: Stay Hidden
The bracelet that had put Darkstalker into a deep sleep so that he could not wake up broke when the comet came by, six months before the book. He asked Moonwatcher to help him escape and told her that he could see all the possible futures. Moon heard someone yelling, "The SkyWing! She's here to kill us all!" and Starflight immediately told her and Kinkajou to hide because he thought it was Scarlet. Instead, Moon went to the source of the commotion and saw a SkyWing that was not Queen Scarlet. Icicle came up from behind her and saw that it was Peril.
Moon learned that the comet apparently woke Darkstalker from the enchanted slumber and that he had enchanted himself to be immortal, which was how he had stayed alive for 2,000 years. Moon then went to Mightyclaws in the art cave to try to learn more about NightWing powers. Darkstalker then learned that legends about him had been extremely exaggerated, and Moon learned that NightWing powers come from the three moons. Darkstalker asked for Moon to set him free from being trapped underground; he claimed he could not use his animus powers to free himself because he did not want to lose his soul. Due to this fear, he had put all of his power in an object, later revealed to be a scroll. Moon then was struck by a vision of dragons dying in a mysterious fire, which caused her to try to stop Winter, Qibli, Kinkajou, and almost anybody else from going into the history room, but Carnelian was too stubborn to listen and was killed by the explosion. The NightWing named Bigtail also died from the blast, and Tamarin and Moon were injured. Winter became suspicious of Moon, wondering how she knew about the explosion and gave her until the end of the next day to provide him with an explanation of how she knew. Turtle guessed about her powers, and Moon admitted that this was true to Turtle, Qibli, and Kinkajou (Winter had stormed off and so he was not around to hear about her powers). Moon learned that a cactus caused the explosion called dragonflame cactus, which explodes when it comes in contact with fire, something Turtle recognized because it was used for bombing the SeaWings' Summer Palace. Overnight, Moon heard the dreamvisitor conversation again, a weird, ominous voice saying that someone must be killed in Jade Mountain Academy, or there would be consequences.
Part 3: The Darkness of Dragons
Moon decided to use her mind-reading powers to help find the killer, aided by Qibli. Moon discovered that Onyx wore a stone that could block mind reading. The stone was called skyfire. Both Onyx and Turtle had them, so she was unable to read their minds. When she and Qibli went back to the prey center, someone attempted but failed to kill Icicle by causing a sharp stalactite to fall on her. The malicious IceWing realized that she was the target and that it was Sora, a MudWing assigned to be her clawmate, who tried to kill her and who was the one who caused the explosion. Qibli and Moon rushed to tell Sora that Icicle was aware, and she wanted to kill her. As a result, Sora and her brother Umber fled the academy.
Moon realized that Icicle was the one who dreamt about the strange, evil voice (who happened to be Ex-Queen Scarlet) and that she was going to kill one of the dragonets of destiny. Realizing that Starflight would be her first target because he was the most vulnerable, she and Qibli dashed to the library before Icicle could kill Starflight. Qibli rushed to stop Icicle before she could manage to get away with killing the blinded NightWing, attempting to stab her with his barbed tail, but he got knocked out by the large IceWing. Then Icicle charged at Moon, choked her, and threatened to kill her. Winter suddenly arrived and attempted to get her to release Moon. When Icicle told him he should be helping her because she was trying to save their brother, Winter faltered. However, he smashed his tail across Icicle's head to save Moonwatcher from his older sister, despite his and his tribe's hatred of NightWings. He questioned how Icicle could work with Queen Scarlet when she was the one holding their brother captive in the first place. This caused Icicle to flee to the rainforest in another attempt to kill a dragonet of destiny, Glory. Hailstorm was Winter's older brother, and because of an incident with the SkyWings when they were both looking for scavenger dens, Hailstorm was captured, leaving Winter to hate himself more than anybody else. Winter had suspicions that Hailstorm was killed by the NightWings when they raided the SkyWing arena to save Starflight. Later that day, Moon gave the skyfire to her friends through Turtle with his bracelet, which contained the skyfire stones. Qibli noticed that Winter had left to find his brother, Hailstorm, who Icicle had said was alive. The Jade Winglet followed him. Winter said that he was going back to the Ice Kingdom for Icicle. Qibli deduced that Icicle probably went to the rainforest to kill Glory, and they (except Turtle) decided to go with Winter to stop Icicle, despite his protests. After Moonwatcher delivered the Jade Mountain Prophecy, it ended with Moonwatcher ready to tell Winter about herself and her powers.