Throughout the book, the third-person narration switches repeatedly from following the human characters to various fairy characters.
Artemis Fowl II is the twelve-year-old son of an Irish crime lord, Artemis Fowl Senior. Artemis's father went missing two years previously after his ship was destroyed by a missile from the Russian Mafia. Artemis's mother, Angeline, was sent into nervous tension and eventually insanity. Also, the Fowl clan has lost their status as billionaires, Artemis the senior having invested a mint from their fortune, shipping cola to Russia to initiate shipping lanes. They sent Artemis Senior a message in the shape of a stolen Stinger missile, launched near the bay of Kola.
Along with his friend and bodyguard Butler, Artemis gathered information on the existence of fairies and their gold. He tracks down a sprite posing as a healer in Ho Chi Minh (or Saigon), Vietnam and acquires a copy of The Book - holy bible of the fairies written in Gnommish.
Meanwhile, an elf by the name of Holly Short, a member of the Lower Elements Police Reconnaissance (LEPrecon for short. This is where the word leprechaun originated), is chasing a troll that managed to reach the surface of the Earth and is attacking an Italian restaurant - fairies live underground. Assisted remotely by a centaur named Foaly and her commander Julius Root, she incapacitates the troll. This uses the last of her magic. After a grilling from Root, he demands that she completes the Ritual, vital for magical creatures to replenish their power.
With Butler's and his sister, Juliet's help, Artemis decodes the Book using ancient Egyptian heiroglyphics, learning of the Ritual in the process, and he and Butler proceed to a site for the Ritual where they find Holly. She attempts to employ the mind-controlling Mesmer, but fails because Artemis and Butler are wearing mirrored sunglasses and Holly is tranquillized. The Lower Elements Police are immediately aware of her disappearance and Root goes to the surface to search for her. He locates her tracker and heads to its location - a whaler off the coast of Dublin. Through an audio/video communicator, Artemis tells Root that he has Holly for ransom. Then, the whaler explodes, and Root narrowly escapes.
A LEP retrieval team is sent to scout Fowl Manor. Using their shield, which allows them to vibrate faster than the eyes can follow, they manage to enter the manor grounds. They are detected by a specialized camera, however, and Artemis sends Butler, who defeats them. Root decides to lay siege to Fowl Manor using a Time-stop, and negotiations are entered - the ransom demand is one metric ton of 24-carat gold. Root lets it be known to Artemis that the People would never relinquish their gold, and that he would eventually send in a bio-bomb to kill Artemis and his comrades to retrieve it, the time-stop being able to contain the short-lived radioactive Solinium flares. Artemis, having read the Book and planned in advance, uses the opportunity to reveal his knowledge, and implies that he can escape the time-stop. He also bluffed the fairies into belief of his 'accidental' invitation, concluding the meeting with; 'None of your kind has the permission to enter while I'm alive.'
One of the laws forbidding fairy entrance to human dwellings without permission, the resulting punishment varying from vomiting and ultimately permanent loss of magic, the attempt to righteously infiltrate Fowl Manor initiated. Root recruited a criminal dwarf called Mulch Diggums to break in. Having lost his magic after he became a thief, Mulch is unaffected by the law. Mulch tunnels underground to reach the house, Foaly helping him by feeding a loop to the cameras, before locating a safe containing a copy of the Book, thus revealing the source of Artemis's extraordinary knowledge of fairy affairs. The Mulch escapes the Manor and fakes his death.
The Fairy Council decide that nothing is working and promote lieutenant Briar Cudgeon to acting Commander in place of Commander Root. Shunting Root off the power seat, Cudgeon sends the troll that was earlier captured by Holly in to force the humans to allow them entry. Meanwhile, Holly remembers she dropped an acorn in her boot and completes the Ritual in her prison cell, regaining her magic, and escaping. After being alerted by Foaly of the troll's entrance, Holly proceeds to again tackle the troll, though not before it had fatally injured Butler. She fails to subjugate it, however, but laid her hand on Butler's arm before falling unconscious, healing him completely. Butler then drew the troll's attention and, strapping on a suit of armor, triumph over the creature. Angered that the troll had decided to dine on Juliet, he only spared its life when the also replenished Holly reminded him he owed her his life.
His plan unraveling unpleasantly, Cudgeon attempted coercion on Foaly for the record of the troll ambush; if it ever reach the hands of the council he would be in big trouble indeed. Root sedated him and resumed control, granting Artemis the aforementioned ransom.
Artemis, glancing up at the attic room, remembered his mother wasting away there, and realized the success of his scheme was tainted; him not being satisfied as he expected himself to be. Therefore, before sending her off, he asks Holly for a wish; Angeline's sanity, which Holly grants at the cost of half the gold. Outside the Manor, Mulch Diggums steals a dozen of gold bars from the ransom the Artemis returned and heads to Los Angelas.
Much to Holly's objection of Juliet's innocence, the LEP stood their earlier ground, and attempt to kill the three to retrieve the rest of the gold, Artemis having 'invited' them in on the sole notion that he is no longer alive, 'blue-rinsing' the house with a biological bomb which kills all organic life and leaves structure unharmed. Artemis, having planned for the rinse, escapes the time-stop with Butler and Juliet by drugging them and himself.
When Butler wakes, he demands an explanation from Artemis, concerned of the risk Artemis had put his sister into, and Artemis explains that by changing one's state of wakefulness in a time-stop, one could overcome its effects. Meanwhile, back in the soon-to-break time-stop, the LEPretrieval team and Commander Root were vomiting on the doorstep. Holly, leading the the team into the manor for the gold, realized then that Artemis has escaped the time-stop alive. He has won, and thus setting her, and maybe the People also, up for a challenge.
Angeline later descends from her attic room, fully cured to sanity, much to Artemis's surprise that Holly had kept her promise despite him chaining her for ransom. She hugged Artemis and apologized for her past actions. Artemis felt a drop of tear on his cheek, but wasn't so sure whose it was. Angeline then reminds Artemis that it was Christmas Day and that she hasn't found him a present yet.
Angeline firing out orders to Butler for remodeling of the manor and for the removal of her things, and asking him of daily happenings, then she talks to him about school. Artemis notes that he would need to polish his schemes to keep them from her, but did not regret it; the return of his mother a Christmas present after all.
At the bottom of each page of the book, a string of symbols appear. These symbols are supposedly Gnommish, but are really part of a substitution cipher which when decoded reveals a message. The message runs throughout the book's pages. It can be deciphered using a section of the book's text which gives a passage in Gnommish from The Book of the People, and then its English translation. The passage speaks of the storyline of this book, and its sequel. The Gnommish cipher key can be found in The Artemis Fowl Files. Strangely, the first book in the series references a small humanoid figure similar to Egyptian heiroglyphics. However, in the Gnommish alphabet, there is no such figure. Actually, the passage speaks only of book 1, and of an odd prophecy, that seems to have been resolved.
There are actually two different translations which are the original and the rewrite. They are as follows.
he prophecies of Ohm phlegm pot cleaner to Frond Elfin King.
I am Ohm, phlegm pot cleaner to the king. But, I am more than that, for I see the future written in the phlegm. For centuries we pixies have read the phlegm but, I am the best there has ever been. My visions are generally of little importance. I foretell outbreaks of troll pox or gas spasms among elderly dwarves. But, sometimes even a poor pot cleaner can see wondrous things. A vision came to me two moons ago when I was gazing deep into his majesties own phlegm pot. I was heating the pot over a flame when the sign appeared. This vision was more vivid and detailed than any I had previously seen. Because of its importance I decided to write it down for posterity. And, so I can say I told you so. I saw an age when the people have been driven underground by the Mud Men. This is what the phelgm told me.
"In this time one shall come among us. Fowl by name and foul by nature. A Mud Man unlike any other. He shall learn our secrets and use them against us".I see him now as plain as day. His face is pale, he has dark eyes, and raven hair. Yet it must be a mistake for he seems a mere youth. Surely no Mud Boy could outwit the people. But, now I see that the boy is not alone. He is aided by a formidable warrior scarred from a thousand battles. This Fowl shall hold the people to ransom for their most precious possession. Gold. And in spite of all our magic there is a chance that he will prevail. For he has discovered how to escape the Time Field. Unfortunately how the story ends I cannot tell. But there was more to see. There is another story to come. Someone will bring the people and Mud Men together. The worst of both races. This fairy's goal is to grind all the creatures of the Earth beneath his boot. And who is this traitor? It is not clear. But, he shall start a war unlike anything the people have ever seen. Those who were enemies shall be united against him. And for the first time there will be Mud Men below ground. I have one clue to his identity, a riddle:
"Goblins shall rise and Haven shall fall A villainous elf is behind it all To find the one who so disappoints Look ye to where the finger points Instead of one face this elf has two Both speak false and none speak true While publicly he lends a helping hand His true aim is to seize command"
I know. Its not very plain is it I don't understand either. But, perhaps in the future all will become clear. Look for a powerhungry elf who has a finger pointed at him during our story. And so this is Ohm's legacy. A warning that may save the world from total destruction. There's not much to work with I know. The details are a bit sketchy. My advice to you is to consult the phlegm. It may be that you are sensitive. I have buried this prophecy with my phlegm pot. If you are not fortunate enough to work as a pot cleaner then there is usually a supply of phlegm every time you have a cold. Here ends the first prophecies of Ohm. But, because of the importance of my visions I shall repeat the prophecies once more. If you have just begun to understand the text then read on. If you have worked out the entire message then congratulations. Now go and save the world.
The first reference to Artemis Fowl in the human media is in a newspaper article from the Dublin Chronicle. Artemis made the paper by solving the riddle of the Mayor of Dublin's chains.
The mayor held a press conference to appeal for help after the city's priceless chains of office were stolen. Artemis managed to persuade his bodyguard to bring him along. when the reporters had finished asking their questions, Artemis raised his hand. The mayor allowed the small boy to ask his question expecting something simple and childlike. Instead Artemis asked him to name three kinds of butterfly.
When the mayor could not answer Artemis stood on his chair and addressed the journalists present. He told them that in his opinion the mayoral chains could not have been stolen from the secure vault or taken from around the mayor's neck without his knowledge. So this man could not be the mayor, he must be an imposter. The proof of this was that the real mayor was a keen butterfly collector and would most certainly have been able to answer Artemis's question. Most journalists laughed but one did not. He suggested that the mayor allow himself to be fingerprinted. The man calling himself mayor panicked and ran.
It was later discovered that this man was indeed an imposter. He was the mayor's own twin brother. The real mayor was being held in a warehouse in the south of the city. The plan was to hold him for a week while his twin's gang looted the mayoral mansion and cashed the insurance cheque for the ceremonial chains.
Artemis Fowl was six years old when he foiled this plan.