On the coast of Ireland, a media frenzy descends on Fowl Manor, where a stolen collection of world-famous relics are linked to wealthy businessman, Artemis Fowl. Arrested at the manor, Mulch Diggums is interrogated by British intelligence and claims that his employer has stolen the powerful "Aculos". Offering to prove the existence of magic, Diggums tells the story of Artemis Fowl, Jr.Three days earlier, Artemis, a 12-year-old genius, lives at Fowl Manor with his widowed father Artemis Sr, who goes missing from his boat, accused of the theft of several priceless artifacts found aboard. Artemis Jr receives a call from a hooded figure. Holding his father captive, the hooded figure gives Artemis three days to recover the Aculos, which Artemis Sr. has stolen and hidden. Domovoi "Dom" Butler, Artemis' bodyguard, shows him a hidden library where generations of Fowls have catalogued proof of the existence of magical creatures.Deep underground in Haven City - home to a civilization of fairies - Mulch, an oversized dwarf thief, encounters Lower Elements Police reconnaissance (LEPrecon) officer Holly Short as he is taken to prison. Commander Julius Root dispatches the LEPrecon force to search for the Aculos, the fairies' greatest resource. Foaly, LEPrecon's centaur technical advisor, discovers an unauthorized creature has reached the surface. Holly is sent to investigate, despite the fact that her father, Beechwood Short, stole the Aculos and was killed. In Martina Franca, Italy, Holly intervenes as a rogue troll and attacks a human wedding party. Using a "time freeze", LEPrecon subdues the troll and wipes the humans' memories.Dom's 12-year-old niece Juliet arrives at the manor. From his father's journal, Artemis learns that Beechwood brought the Aculos to Artemis Sr. to keep it from the hooded figure, revealed to be Opal Koboi, a fairy planning to wipe out humankind. Artemis sends Dom to stakeout the Hill of Tara. Holly, determined to clear her father's name, disobeys orders and flies to the Hill of Tara, where she finds Beechwood's ID tag, but is captured by Dom and imprisoned inside the manor.Root and an army of LEPrecon officers seal Fowl Manor in a time freeze, but Artemis and Dom fight them off using Holly's equipment. Artemis demands the Aculos in exchange for Holly's release, forbidding fairies to enter his home while he is alive. Bound by fairy rules, Root retrieves Mulch from prison, offering him a reduced sentence to infiltrate Fowl Manor. Mulch tunnels inside and breaks into Artemis Sr.'s safe, finding the Aculos, while Artemis frees Holly and asks for her help. Lieutenant Briar Cudgeon, a spy for Koboi, seizes command of LEPrecon and releases the captured troll into the house, jamming all magic inside.Mulch swallows the Aculos as Artemis, Holly, Juliet, and Dom evade the troll, which is subdued. Pushing Artemis out of the troll's way, Dom is mortally wounded. Against orders, Holly's fellow officers unblock her magic, and she revives Dom. Mulch and the LEPrecon army escape as the time freeze collapses. Left with the Aculos, Artemis refuses to give it to Koboi, and Holly agrees to use it to rescue Artemis' father. As Koboi attempts to kill Artemis Sr., Holly summons him to Fowl Manor.Artemis Sr. tells Holly that her father gave his life to protect the Aculos, giving her a list of Koboi's accomplices. Holly returns the Aculos to Haven City, where Root, back in command, directs her to investigate every name on the list. Artemis calls Koboi, promising to come after her. Mulch's interrogator offers him freedom in exchange for help capturing Artemis Sr., but Mulch reveals that Artemis arranged his arrest to prove the incident to the authorities, and confirms the existence of magic on camera. As the interrogator calls for backup, the Fowls' helicopter rescues Mulch and, joined by Holly, they fly off.