The story begins with the pixie genius Opal Koboi in an asylum, appearing to be in a coma after the collapse of her revolution. In reality, she is actually in a self-induced healing coma, a type of that coma she learnt at the age of fourteen, which is young even by human standards, much less fairy. Though Opal is convinced that the her rebellion in the second book would succeed, she has still prepared a contingency plan which involves setting two of her most trusted employees, Mervall and Descant Brill, iconic twin fairies, to work in an asylum and creating an account of money to be opened in the case that the revolution failed and she did go into a coma. After spending a record amount of time in the coma, she has her two accomplices in the J. Argon Clinic replace her with a brain-dead clone. The clone looks exactly like Opal, and with no one the wiser, she escapes.
She then progresses to frame Captain Holly Short with the murder of her Commander, Julius Root by having her take an extremely difficult, if not impossible shot, at the bomb vest that has attached itself to Root's chest. Holly, given a chance to free her commander, takes the shot perfectly but the bomb explodes anyway. Meanwhile, no audio is available outside in Foaly's command center, and for all purposes, everyone assumes Holly has just shot Root. Realizing all this, Holly takes off to find Artemis above ground, further deepening the mistrust several officers have for her. Opal then also sends a Bio-Bomb towards the fourteen-year-old criminal mastermind Artemis Fowl Junior.
Meanwhile, having lost his memories, Artemis Fowl Jr. has now retained some of his rather crueler characteristics from before his meeting with the fairy race. He is currently in a bank in Switzerland stealing an expensive painting stored in their vaults. Luckily for Artemis, his faithful bodyguard Butler saves him from the bio-bomb, though Butler loses his consciousness after a perilous fall from their balcony, and Artemis is severely injured. After fleeing Haven and failing to secure Artemis before the bomb had been detonated, Holly realizes Opal had lured her above ground to increase the suspicion laid on her. She then barely survives the second bio-bomb, using her helmet to suppress the solinium flares. She later noticed a coagulating group of curious humans near the fall and found Artemis. Her saving herself using her helmet also has the additional affect of everyone in the command center assuming her to be dead, due to the fact that all sensors that check Human vitals are stored in the Helmet.
After healing him, she takes Artemis to the Temple Bar area, one of the fairies' many Cham Pods. She tries, but fails to bring back Artemis's memories of The People. Despite this, Artemis agrees to help Holly on the caveat that she pay him fairy gold, and proceeds to leave a message for the then unavailable Butler through the Fowl Manor phone. Unfortunately, the pod where Artemis and Holly are hiding out, is blown apart by Opal and her henchmen before he could finish; she has been following them in a stealth-shuttle. Two things go in Artemis' favor, however. He left his cell phone connected to his home and Holly did not bring Butler, Butler being too big to be removed without suspicion.
Opal once again tries to kill both Artemis and Holly by stranding them in the Eleven Wonders Theme Park. Spraying them with troll pheromone when the once prosperous park is now inhabited by trolls, the creatures would soon realize the two were not the female of their kind and proceed to devour them instead. Just before they are about to be eaten, Holly and Artemis are rescued by Butler and Mulch Diggums, who, after escaping the prison vessel transporting him, traveled to Fowl Manor to present Artemis with the memories stored on the disc he received. Caught in the act by Butler, he offered the disc to the bodyguard and, Butler's memories now re-vitalized, together they raced to the Eleven Wonders.
After being pulled up to the ship, Artemis acknowledges Holly as a friend and cancels the earlier payment deal, saying 'Opal must be stopped'. His memories restored after he has seen what was on the disc, they proceed to eliminate Opal's destructive scheme. They locate her in E7, her plan to create an inter-species war and destroying Haven almost at fruition. Meanwhile, Foaly discovers Opal's clever plan and convinces the council and Ark Sool to send a supersonic attack ship to check on Holly. While Artemis manages to stop Opal, just before her ship explodes, she fires two torpedoes at their ship, which then turn upon the Supersonic Attack Shuttle flown by Major Trouble Kelp. Having safely avoided the missiles, Trouble is ordered by Ark Sool to attack Holly. Trouble disobeys, however, and gives Holly a chance to prove her innocence through a communication rod connecting the two ships.
Opal escapes to above-ground and is later captured and held captive in Atlantis, her magic now un-replenishable due to the fact that she has removed the organ that aids re-generation of magic in fairies. Her henchmen, Mervall and Descant, are taken into custody earlier, Opal having abandoned them when their ship exploded, and confess readily. Though Holly is later cleared of all charges, she is frustrated by her new commander, Ark Sool, who did not even give her the opportunity to pay her last respects to Commander Root, a notion she names as the worst Sool could ever have done to her, and resigns, becoming a private detective along with the dwarf Mulch Diggums, who was also acquitted of all charges. She maintained a secret correspondence with Artemis, who has finally appeared to redevelop some morals, giving to the public the priceless artwork he stole in the beginning of the book. This may have been just a copy because it was sent in regular mail, and Artemis has had a reputation of faking impressionist paintings.
Most Artemis Fowl books have Gnommish hidden somewhere on the cover, and The Opal Deception is no different. The cover portrays chute E37, and Gnommish is running up the sides from the center on the right if you look at the cover from a special angle under the light (first US edition) The Gnommish says "Opal wants revenge", and can be found in three other spots on the cover in straight lines.
- "A recruitment letter from the centaur Foaly, technical consultant to the Lower Elements Police-
- Trusted ally, if you have decoded this Gnomish message, then you are a deputy officer in the Lower Elements Police. You will not be aware of this fact because it is the practice of the LEP to mindwipe our human allies. We do this so they cannot remember being recruited. If you cannot remember the Fairy People, or our underground city, then you cannot betray our existence to the greedy humans. Of course, not all humans are greedy. You, deputy, are a noble member of your species. And clever too. Our intelligence department studied your file and concluded they you were suitable for LEP membership. At the moment, you are only a deputy officer. To become a fully fledged officer, you must complete four tasks.
- Decode this message. Something you are well on your way to completing.
- Save the life of a member of another species. You can complete this task in any number of ways: open a window to release a trapped fly, build a bird bath in your garden, release a mouse from a trap...
- Achieve a perfect score on a school test, or homework assignments. In this job, you need to be smart, as well as fit.
- Wash yourself every day for a week. This is a difficult assignment, especially for you boys who do not like contact with water. If you are going to work underground often in cramped tunnels, you will appreciate a partner who does not smell like a hermit dwarf.
- Once you have completed these tasks, you must summon your recruiting officer in the ancient fashion:
- Go to your back yard or nearest green area.
- Make sure you are not being watched.
- Find a soft spot of ground and burrow a six inch hole with a broom handle or short stick. When your hole is ready, tap out the letters "L," "E," "P" in Morse code:
- "L" tap, tap, wiggle, tap, "E," wiggle, wiggle, tap "P" tap wiggle drill.
- Do this at least a hundred times, and our underground sensors will pick up the vibration and send up an L. E. P. officer with your uniform and orders.
- Good luck, deputy!
This is not part of the letter but don't you think it would take a really long time for the LEP officer to arrive or they will not pick it up?
Although it's hard to prove it's possible that "Foaly" just wanted to do this so that any human who dechipered it would improve the human race in some small way.
Once again there is also a rewrite which has failed to have been mentioned.
There has never been a regulated scientific study of dwarf's special abilities. What we know about them is based on folklore and hearsay. The most famous of these abilities is the dwarf tunneling method by which they eat dirt and air, before expelling them out the other end.
Though the actual force of this expulsion has never been measured, several witnesses have reported windows breaking more than twenty metres away. It is said that a master recycler can fine tune his gas emissions so that instead of a widespread blast of flatulence he shoots out a concebtrated column of wind. Legend has it that one such master recycler (a certain Blurt Miggums) was so accurate with these columns that he could turn on a light switch from the other side of the room.
Dwarfs themselves use casual terms to refer to the strength of their gas emissions. A "shirt flapper" is a gentle emission that would barely inflate a child's balloon. A "pants ripper", a sturdier blast and would certainly blow a hole in even the sturdiest material . A "nought to sixty" is a right whopper and could accelerate whoever dropped it to dangerous speeds. A "strap yourself down" is about as strong as it gets and could help a dwarf achieve flight. And finally the legendary "dark side of the moon" or simply "dark side". If released on a mountain top it could put a dwarf into orbit.There is no evidence that a dark side is anything more than a myth. All the same if you see a dwarf on a mountain with a red face, take cover. You can't be too careful around dwarf wind.