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Menolly, a young fisher's daughter, had dreamed all her life of learning the Harper's craft. When her stern father denied Menolly's destiny, she fled Half Circle Hold just as Pern was struck again by the deadly danger of Threadfall, the killing ropes of death that fall from a nearby star. Taking shelter in a cave by the sea, Menolly made a miraculous discovery that ensured her a new home among the master musicians of Pern's Harper Hall.
Dragonsong opens with the death of Petiron, the harper at Half-Circle Sea Hold. Until a replacement harper can be sent to the hold, Menolly, the daughter of the Sea Holder Yanus and Petiron's favourite student, is begrudgingly chosen to teach the children. However, Menolly is expected to put aside all hopes of a musical future, as women don't become harpers, and as such she is forbidden to practise or play any instruments - despite Petiron approving her music and even sending it to the Harper Hall.
Despite this, Menolly plays in secret, and leaves her tunes for the new harper to discover. Unknown to her, her mother Mavi is aware of this, and later intervenes, and one day Yanus catches her, beating her with his belt and confiscating her gitar. Following this, Menolly is sent to gather fresh herbs from the lands surrounding Half-Circle Sea Hold. While out, Menolly witnesses the mating flight of a queen fire lizard, a creature thought mythical, though occasionally reported by the seaholders. As she returns to Half-Circle Sea Hold, Menolly discovers that Petiron's replacement, Elgion, has arrived.
A few days later, Menolly cuts her hand while gutting packtails, and her hand becomes infected. Mavi treats it, but informs Menolly that her hand has been crippled as a result, and she will likely never play music again. When Menolly heals, she returns to harvesting herbs - often running ahead of the others so she can be alone. On one occasion, she ends up at a cove near the Dragon Stones, a natural rock feature along the coast of Nerat, and witnesses a queen fire lizard flying at the water, rising with the tide.
Climbing down to the cove, Menolly discovers the reason for the queen's acts: it has laid a clutch of eggs on the beach that will be swept away by the rising tide. The queen and several other fire lizards at first fly at Menolly, thinking her a threat to the eggs, but she inadvertently soothes them by singing, and aids in rescuing the eggs by carrying them to a cave, before returning home.
Around this time, Elgion begins asking Yanus who taught the children in his stead, as he believes they would make a good harper, but Yanus lies and says it was a fosterling from another hold. Unknown to Yanus, Elgion has been instructed to stir up change at Half-Circle Sea Hold - Masterharper Robinton believing that holds all across Pern need to become open to new ways of thinking - and also to find who wrote the music Petiron sent to the Harper Hall.
At a dinner, Elgion calls every member of Half-Circle Sea Hold to sing, but Mavi forbids Menolly from singing any louder than the women of the hold normally sing. In anger, Menolly leaves the hall, and sneaks out early the following morning to return to the cove. Halfway to the cove, Thread begins falling, and Menolly is forced to shelter in the fire-lizard cave, where the eggs are hatching. The hatchlings are hungry, and attempt to leave the cave as Thread falls over it. In an attempt to prevent their deaths, Menolly begins feeding the hatchlings with the food she has with her. As Threadfall ends, the queen fire-lizard guides the others out, and Menolly decides to remain in the cave.
Menolly's absence is eventually noticed at Half-Circle Sea Hold, and the inhabitants wonder if she was killed by Thread. Elgion talks with her parents, and they conclude she is probably hiding in a cave along the Nerat coast, as she knows the area well. Two days after the Threadfall Menolly has not returned, and it is ultimately decided not to look for her. Elgion is unsatisfied with this, and manages to tell the dragonriders of the situation when N'ton arrives from Benden Weyr to ask him to search the coast for fire lizards, recently "rediscovered" on the Southern Continent.
Meanwhile, in the cave, Menolly wakes to find nine fire lizard hatchlings resting around her - she has Impressed them. Instead of returning to Half-Circle Sea Hold, she decides to remain in the cave, emerging only to get supplies for herself and the fire-lizards. In time, she names her fire lizards and gets into the habit of singing to them - especially once they sing back.
At Half-Circle Sea Hold, Elgion strikes up a friendship with Menolly's brother Alemi, who is keen to learn about the outside world. Alemi teaches Elgion how to sail, and at Elgion's urging, the two end up sailing to the Dragon Stones - Elgion is planning to search for fire lizards there. At the Dragon Stones, Elgion and Alemi overhear music coming from the shore - Menolly playing from within the cave. The conversation turns to Menolly, and Elgion soon realises that she was the teacher. Alemi tells him that Yanus thought Menolly acting as a harper was disgraceful, and also adds that he feels Menolly is better off away from the hold. They return to Half-Circle Sea Hold, where Elgion sets up a signal for N'ton, and plans to head to the cove near the Dragon Stones to see if Menolly was playing the music he heard.
At the cave, Menolly is woken by the feelings of hunger from her fire-lizards, and heads out to find food. While she is out, Thread begins falling, and Menolly begins running for the safety of the cave - despite knowing it is too far away. As she reaches the cove, she is seen and rescued by T'gran, a dragonrider, who takes her to Benden Weyr. Upon arrival, Menolly finds she cannot walk without great pain - her old boots tore as she was fleeing the Thread, and her feet are lacerated - and so T'gran takes her to be treated by Manora, who puts her to sleep with a dose of Fellis. Also at Benden Weyr is Elgion - having been rescued from Thread while searching for Menolly - who uses his time there as a chance to observe Weyr life.
When Menolly wakes, she tells her fire-lizards to hide, and later requests from Manora that nobody tell her family she is here. Menolly is later cared for by Mirrim, a child her age who lives at Benden Weyr, and the two become friends. Mirrim later looks over Menolly's "crippled" hand, and her pronouncement causes Menolly to realise Mavi may have intentionally let her hand heal badly to prevent her from playing music.
Over time, Menolly's feet heal, and she offers to help with the weyrbred children, realizing as she works that she is at last free from the restrictions of her home. Menolly notes the mood in the Weyr is odd, and she is later told by Sanra - another inhabitant of the Weyr - about the recent events on Pern, including the deaths of Prideth and Wirenth, and how they fear Wirenth's rider Brekke - foster mother of Mirrim - who has since gone catatonic, will lose her mind as a result. To remedy this, they are controversially planning to place her as a candidate in the next Hatching.
Menolly is unable to keep her fire lizards secret for much longer, and she is approached by Lessa, who asks her about where she found them, before sending her to the cove with T'gellan to try and find another fire lizard clutch, which they do. Lessa plans to hand these eggs out to the Lord Holders and Craftmasters who attend the Hatching. Lessa states Menolly belongs in Benden Weyr as a result of her fire lizards and Menolly becomes overwhelmed to the point of tears by how nice everyone is being to her. After calming down, Menolly joins Mirrim and T'gellan in the Dining Caverns, and is called to sing with Oharan - along with her fire lizards, who join in - when they overhear her humming a harmony to his tune.
The next morning, Menolly helps the inhabitants of the Weyr prepare for the Hatching festivities. T'gellan takes Menolly to the Hatching Grounds, where she witnesses Brekke emerge from her catatonic state - failing to Impress -, and young Jaxom of Ruatha Hold leap onto the sands and break open an egg ignored by the others, inadvertently Impressing the white hatchling inside.
Following the Hatching, Menolly meets a harper who carries her to the Dining Caverns when he sees she is having trouble walking. In the Dining Caverns, it is revealed that the man is no less than Masterharper Robinton, but he leaves before Menolly can talk with him. Mirrim and T'gellan arrive to talk with Menolly about the Hatching - Mirrim has been with the recovering Brekke - before Menolly is taken to the Kitchen Caverns to help distribute the fire lizard eggs.
At the same time, Elgion plays music with Oharan, before going over to talk with T'gellan about where he found the fire lizard eggs. T'gellan ends up telling him about Menolly, and Elgion rushes to find Robinton and inform him that Menolly is Petiron's "lost apprentice".
Much later in the evening, Menolly is waiting for Robinton to return for his fire lizard egg. Oharan approaches her and asks her to sing with him, which she does. He then switches to one of her songs, and Robinton enters and asks she play for him, before inviting her to come back with him to the Harper Hall and become a harper.
- Main article: List of characters in Dragonsong