NOTE: This Spoiler was sent in by Pook!
This is a sequel to "Wicked", Maguire's book that was adapted into a Tony-award winning musical (although the book and musical differ quite widely).
As the book opens it is about ten years after the death of Elphaba, The Wicked Witch of the West, and there has been a rash of attacks on novice Maunts (nuns) of the Church of Glinda (named for the Saint that Glinda was named after, not the Glinda we know herself) where they are killed and their faces are scraped off. This makes a travelling group quite nervous as they travel the grasslands where it occured. What they find instead, though, is a young man who has broken every bone in his body, is naked, but is barely alive.
They take him back to the Mauntery where he is tended to by the Maunts. They assign a young Quadling novice named Candle who never speaks to play her odd broken instrument the Domignion for him, and the two doctors who were looking after him, Sister Apothecaire and Sister Doctor, are sent out into the grasslands to find out the cause of the face scrapings. Candle is given a Pfenix feather by a dying Pfenix who was on his way to some kind of critical conference of the Birds (talking ones) but was fatally injured on the way by something. The feather completes the Domignion and as it turns out Candle is not stupid as everyone assumed, but has some kind of magical power over music. She plays for the young man, and the music helps guide him through his memories and towards finding himself once more.
It turns out he is Liir, the son of Elphaba and Fiyero, which is stated flat out in the first book although this book makes quite a business of everyone including Liir not knowing that or wondering if that is actually the case. He remembers back to just after Elphaba died, and escorting Dorothy and her entourage back to the Emerald City in the hopes of finding his half-sister Nor, who was taken by the Wizard's men led by a Commander Cherrystone. On the way they meet Princess Nastoya, leader of the nomadic Scrow people, who is an Elephant who willed her body to be human to hide from the purges of intelligent Animals by the Wizard. But now she is dying and the Wizard has gone, and she wants to be an Elephant again. Liir carries Elphaba's broom and cape, so she assumes that he too is a Witch, but Liir has no power that he is aware of. He's barely an adolescent at the time and very angsty and existential about his life, wondering what to do with it now that Elphaba is gone, not knowing his place in the world. He half-promises under pressure to try to do something. After an arduous journey they arrive in the Emerald City, which is filled with vagrants, beggars and homeless people. Dorothy goes home without saying goodbye to Liir, who had wanted to go with her even though he didn't much get along with her and thought she was kind of dumb, and he is upset. He finds the Scarecrow again, who warns him to leave town since Glinda is now temporarily in charge and the city will be purged of "undesireable" people. Liir catches sight of Glinda herself, though, and resolves to see if she knows about Nor.
He goes to see her, and although she doesn't know about her case specifically she agrees to help him get into Southstairs, the large underground prison of the Emerald City to look for her. She is also quite torn up about Elphaba's death. She takes him to see none other than Commander Cherrystone, who doesn't seem to remember Liir at all but seems nice and affable. He assigns a guide for Liir in Southstairs who turns out to be Shell, Elphaba's younger brother. He describes himself as a doctor, but what he seems to be doing is drugging and forcing the women in Southstairs into sex. He leads Liir to the man in charge of Southstairs, a rather corrupt individual with an Elf servant who grudgingly helps Liir find the area where Nor was kept with as many Animals as the Wizard could round up, guilty of anything or not. They interrogate an ailing Sow by killing one of her Piglets, and this sends Liir reeling. She reveals that Nor escaped by hiding under the rotting bodies of two Hogs who were protesting being killed to be eaten in a palace holiday meal. Liir is discouraged at finding a dead end and horrified by the death of the Piglet, and when Shell and the prisonmaster leave Liir more or less to rot in Southstairs forever he almost subconsciously gets on the Broom and flies out.
After flying around for a while, while he loves the freedom, he can't think of anything to do with himself so he just hangs out in the Emerald City. He is spotted by a young man named Trism in the Emerald City armed forces who advises him to join the army and gives him good advice on being successfully recruited. Liir joins up and mostly keeps to himself, quietly resenting his fellow soldiers who have good families and keeping his secrets, more or less forgetting his promises to find Nor and to Princess Nastoya. During that time Glinda abdicates in favor of a Scarecrow who Liir is not very surpised to see is not the same Scarecrow that accompanied Dorothy. He grows close to Commander Cherrystone, who becomes like a surrogate father to him. Years later he sees Trism again and they go out drinking, and Trism lets it slip that he is working on a super secret project for the army involving dragons. Liir is too drunk to get home and Trism gets Shell, who has showed up, to take him. One day the unit moves out and goes to the Quadling country (a Quadling figured in significantly in Elphaba's family in "Wicked" and her family spent a lot of time there) where they presumably are supposed to find out about the disappearance of the Ambassador from the Emerald City's family, but instead they end up just stationed there for several years. While they are gone, a Holy Emperor takes the throne after an "unfortunate accident" with the Scarecrow and fire but this doesn't make much difference to the men there until Cherrystone receives orders to start trouble with the Quadling people. He orders Liir to take a squad and set fire to a bridge that is like a whole city to the Quadlings. Liir does as he's told, but upon seeing the people burning to death and a couple pitching their daughter into the predator-infested waters to save her he deserts the army and goes wandering.
He eventually finds his way back to Kiama Ko, Fiyero's castle that Elphaba lived in until her death. He stays there a while with the aging Nanny who raised Elphaba and Chistery the winged Monkey who has now learned to talk almost perfectly in Elphaba's absence, although he is the only of the winged monkeys who has. While he's in Elphaba's tower room he sees a vision in her enchanted glass of her in her room at the Mauntery rocking a cradle with him in it with her foot while still being in a state of comatose shock from Fiyero's and Madame Morrible's deaths. He also finds Fiyero's boots in her closet with a drawing of Nor in them. He resolves to go find her again now that he's sure about his parentage. A Swan shows up, however, claiming she was attacked by dragons that are preventing the Conference of the Birds from forming to figure out how to defend themselves from them. Liir promises to go in her stead and preach her message of unity between all intelligent creatures. He finds them living in terror of leaving their meeting spot because of dragon attacks and reluctantly promises to try and help.
As he's flying, though, he too is attacked by dragons. They take his broom and his cape and beat him almost to death and fly away. This brings us to present day.
Meanwhile, while all this is going on we occasionally visit Candle, trying desperately to keep Liir alive while he wanders through his memories including warming him with her own body at a critical point, and Sisters Doctor and Apothecaire who meet the Scrow people as well, who think the rival nomad clans of the Yunamata are responsible for the face scrapings and vice versa. They meet Princess Nastoya who is much the worse for wear after ten years of dying and confirm that they have Liir who has been avoiding his promise. They make her comfortable and promise to go find him.
When Liir finally comes to Mother Yackle, a maunt who had a major behind the scenes in just about everything in Wicked has him leave with Candle as soldiers are coming to find him. He and Candle go to a small farm and set up house, and he falls in love with her - until she reveals that she is pregnant. She says that the baby is his, but he says it can't be since they never slept together and she's just setting him up. He finally resolves to leave and finally fulfill his obligations to everyone, leaving Candle with a promise to return.
First he heads to the Emerald City, where he meets Trism again by accident. Trism attacks him for being a deserter and because he is miserable in his job as the chief dragon wrangler for the Holy Emperor...who turns out to be Shell, being about a million times worse of a despot than the Wizard ever was. He has been commanding the dragons to attack people and places and animals and scrape off the faces of missionaries to make the Yunamata and Scrow fight. Liir convinces him to help him kill the dragons once and for all. They sneak in and feed them poisoned food and retrieve the scraped faces, which the Emperor has had mounted in rings for display. They also fetch Liir's broom and cape. They escape together and become involved physically, although they both seem ambivalent about it being a romantic relationship for different reasons. Liir advises him to find the farm where Candle is staying and goes on to find the Conference of Birds.
He relays the message that they are safe from dragons, although not so much from the people who unleashed them. He convinces them to fly with him to the Emerald City, where they fly in a huge Elphaba-shaped formation and scream "Elphaba Lives!" at the city, which has been turning up as graffiti on city walls a lot lately. Then they disband, except for a large gray goose that decides he's Liir's familiar. He goes to find Candle and finds out that Trism had been there but left again, and is worried that they may have fallen in love or hated each other and he's not sure which he fears more. A group of Scrow is also there with Princess Nastoya, and Liir persuades Candle to play her music to reshape her. She uses her talents to get the scraped faces to sing. This works and Nastoya dies an Elephant at last, and they leave. Then Soldiers approach, and Liir flees to the Mauntery leaving Candle alone again. The Maunt in charge rallies her fellow Maunts to fight the Emperor and as it turns out Glinda arrives also, and uses her power and wealth from her elderly but deceased husband to get the soldiers to stay back. Liir goes back to the farm looking for Candle but finds nothing but that she left in a hurry. He finds his cloak with what appears to be a dead baby wrapped inside, but realizes that the baby girl is actually alive. Washing her up, she cleans up green.