In Chapter 1, twelve-year-old criminal mastermind Artemis Fowl and his assistant Julius Butler are in Ho Chi Minh City, Vietnam, looking for a fairy. They meet with their contact, Nguyen, who leads them to her hiding spot, where she has been posing as a healer. She is an alcoholic, and refuses to do business with Artemis until he hands her a bottle of Irish whiskey. Artemis knows that she has lost her magical powers due to centuries of alcohol dependence. However, the whiskey has been laced with holy water, which is fatal to fairies. Artemis tells her that he will give her an antidote to the poison, as well as a serum which will return her magical powers to her, if they let her photograph her Book, which contains the secrets of the fairy world. She agrees, and Butler and Artemis photograph the Book before heading back home.
In Chapter 2, Artemis and Butler arrive back to the Fowl Manor. Artemis visits his mother, who has been on bed rest for nearly a year. She recognizes him at first, but quickly becomes frantic as she explains to him that she can hear voices. Artemis can hear her terrified sobs as he walks away from her room. In his study, Artemis spends several hours translating the book. He does not get lucky for a long time until he realizes that the characters in the book are very similar to Egyptian hieroglyphics. After this success, he also discovers that the book cannot be read from left to right and instead is written in a spiral. Artemis is forced to do all of these translations by hand because there is no computer program that will recognize the language. Eventually, he succeeds, and we discover what he wants to get out of the Book: fairy gold, in the hope that it will restore his family name.
in Chapter 3, we meet a new character, Officer Holly Root of the Lower Elements Police. She is an elf who lives underground with the rest of the fairy population, who refer to themselves as the People. When she gets to work, her boss, Commander Root, gives her a hard time for being a few minutes late and threatens to demote her from Recon to Traffic duty. However, she convinces him to give her a second chance, presented in the form of a loose troll which has made its way aboveground, on its way to terrorize the human world. Root tells Holly that by no means is she meant to retrieve the troll by herself; she merely is meant to do recon before the Retrieval team can come and fix the mess. However, once Holly tracks down the troll, she sees that he has broken into an Italian restaurant and she has to think on her feet. She disobeys Root's orders and tries to fight the troll herself. Chaos ensues, but she is eventually able to subdue the troll and put the humans in the restaurant to sleep. Holly is so exhausted following her struggle with the troll that she falls asleep alongside them. Her magical powers are completely depleted—it has been four years since she has performed a ritual that all fairies need to complete to rejuvenate their magical powers. She wakes to find that the Retrieval squad has already arrived, and though the restaurant is in a state of disarray, Root tells her that she did a good job, considering the situation. He then commands her to go complete the ritual that night, as soon as possible. Holly sets off to do so.
In Chapter 4, Holly makes her way to Ireland to complete the Ritual. She finds a secluded spot that is hard to access by foot. Before her magical abilities can be returned to her, however, she is ambushed by Artemis and Butler, who have been staking out for over four months. Butler shoots her with a tranquilizer dart right at the moment that she is bending toward the ground to pick up an acorn. Holly and Artemis exchange a few words, and Holly tries the mesmer spell on them. However, she is unsuccessful, probably because Artemis and Butler are wearing reflective sunglasses. Ultimately, Butler successfully hits her with a dart and Holly falls unconscious. Butler stuffs her unconscious body into a duffel bag and Artemis picks up her fallen helmet.
In Chapter 5, Foaly tells Commander Root that Holly has lost contact and has likely been abducted by a pair of humans. Commander Root jumps into action and puts himself back in the field. This is an extremely dangerous and delicate mission—the fate of the People is at risk and Holly's life is in danger. Meanwhile, Artemis and Butler go to the Dublin docks and Artemis asks Butler to create a diversion. He does so by picking a fight with six burly dockhands and quickly incapacitates them. Butler makes it back to the car and finds Artemis. Holly wakes up in Fowl manor, where Juliet is watching her with a large pair of reflective glasses on her face. Holly tries to convince Juliet to take off the glasses so that the mesmer will work on her, but Artemis has advised Juliet to not take off the glasses under any circumstances. Root tracks Holly's locator to an abandoned whaling ship and finds that Holly is not there. Instead, Artemis communicates with him through a pinhole camera and speaker, warning Root that he is not to be trifled with. He then sets off some explosives, and Root barely escapes.
In Chapter 6, Artemis and the LEP officers butt heads. Twelve officers from LEPrecon One approach Fowl Manor with their shields on in their first attempt to extract Holly. Artemis gives Butler a modified version of Holly's helmet, which includes a setting that counteracts shields. The Retrieval Squad does not expect Butler to be able to see them, and he quickly disarms them. He leaves only one member of the squad conscious, and he gives him a warning—next time, he will simply take them all out with a sniper gun. He then allows the fairies to retrieve their injured officers. He tells them to send in a negotiator to talk to Artemis. Meanwhile, in her cell, Holly discovers the acorn that she picked up during the Ritual in her boot. She comes up with a plan, and begins throwing her bed against the concrete floor of her cell in an attempt to reach some fresh ground. If she is able to plant the acorn while the moon is still in the sky, her powers will be returned to her. Commander Root eventually approaches Fowl Manor. He and Artemis negotiate with each other, and Artemis tells Root that he wants one ton of gold in repayment for releasing Holly. Root tells him that he will need time to think about Artemis's demands. Artemis also tells Root that he knows about the Time Stop and the blue rinse—he is not worried, however, because he knows how to escape it. Back at Ops, two behavioral analysts analyze Artemis's movements during the negotiation and determine that Artemis is not lying. Backed against a wall, Root decides that it is time to break protocol.
In Chapter 7, Root is finally able to gain an upper hand on Artemis. He sends Mulch Diggums, a kleptomaniac dwarf, into the manor. Root convinces Mulch to complete this job by offering him a shortened sentence in jail. Mulch is able to get in by digging a tunnel underground. While Mulch is inside the manor, he finds a safe where Artemis has stashed a copy of the Book. He is able to escape by hitting Butler with excrement on his way out. Meanwhile, Holly is finally able to break out of the concrete floor of her cell and complete the Ritual. When her powers are returned to her, she mesmers Juliet, locking the girl in her cell. Safely shielded, she is now free to roam the manor. Artemis watches all of this unfold from a surveillance room upstairs. On his way out of the manor, Mulch deceives Foaly and Root by pretending there is a cave-in and putting his iris-cam on a rabbit. He escapes towards freedom.
In Chapter 8, the behavioral analysts tell Root that they believe Artemis has made a mistake. They pull up the recording of the negotiation between Artemis and Root and point out that Artemis says that no fairy is welcome in his home as long as he is alive. This is a loophole: as the analysts point out, this means that the fairies are allowed in his home after he has died. Root comes up with a new plan: give Artemis the ransom, have him release Holly, apply the blue rinse and kill the humans, and take back the gold. Before they can implement it, however, Cudgeon appears to tell Root that he has spoken with the Council and they placed him in charge, thus demoting Root. Root feels as if his friend of 600 years has stabbed him in the back. Cudgeon's plan is to release the troll that Holly tracked down in Chapter 3 into the manor, thus forcing all of the humans outdoors. Root warns Cudgeon that this is a bad plan, but he follows through with it anyway. After Cudgeon's LEP squad releases the troll in Fowl Manor, it zooms in on Butler and the mesmered Juliet. Butler is gravely injured. Before the troll can harm Juliet, however, Holly arrives and fights the troll. He injures her, and as her magic works to heal her, she heals Butler. Soon, Butler jumps to his feet and is given a second chance to fight the troll and save his sister. He straps on a Medieval suit of armor and fights the troll. Eventually, the troll is subdued. Right before Butler kills the troll, Holly tells him to stop. Butler only agrees because he owes Holly one after she saves his life. Finally, he rolls the unconscious troll out the front door.
In Chapter 9, Cudgeon is taken off of the case due to his disastrous failure. The Council finally agrees to send the ransom to Commander Root, who informs Artemis that it will be arriving. Foaly warns Artemis one last time about the blue rinse, but he maintains that he will be able to escape it. The LEP team sends the gold into the manor on a self-driving trolley. Artemis has Butler and Juliet unload it into the manor. Before they release Holly, however, Artemis asks her for one last wish. In return, he releases her with half of the gold. Holly tries to convince commander Root not to deploy the blue rinse, but he tells her they have no other choice. Ultimately, Foaly detonates the bio-bomb, and the Retrieval Squad get ready to enter the manor and recover the second half of the gold. However, they find themselves unable to enter, still magically bound by the fact that Artemis said that no fairy was allowed in his home as long as he was alive. It becomes apparent to them that somehow, Artemis, Butler, and Juliet survived the blue rinse. They are forced to leave the gold with Artemis—according to the Book, if a human is able to attain fairy gold and survive, it is his to keep. When Artemis awakes, Butler questions him about the sleeping pills. Artemis tells him that is how they survived the bio-bomb: they escaped the Time Field by changing their state of consciousness. Artemis asks Butler if he forgives him, and Butler says he does but makes Artemis promise that they will never deal with fairies again. Artemis's mother comes downstairs and she seems to be acting normal again. Artemis's final request to Holly was that she would heal his mother; evidently, it worked. Artemis's mother tells him it is Christmas, and Artemis feels as if he has been given the best gift he could ever get.