On the picturesque coast of Ireland, chaos erupts at Fowl Manor as a media frenzy takes hold, all stemming from a collection of world-renowned relics that have been stolen and linked to the influential businessman, Artemis Fowl Sr.. Amid the turmoil, Mulch Diggums is apprehended at the manor, and during his interrogation by British intelligence, he claims that his employer has snatched the potent "Aculos". In order to validate the existence of magic, Diggums relays the story of Artemis Fowl Jr..
Just three days prior, we meet the brilliant 12-year-old Artemis Fowl Jr., who resides with his widowed father, Artemis Sr., at Fowl Manor. A distressing turn of events occurs when his father mysteriously vanishes from his boat, accused of pilfering various priceless artifacts present onboard. In a moment of urgency, Artemis Jr. receives a call from a mysterious, hooded figure, who, while holding his father hostage, demands the return of the Aculos—a powerful artifact that Artemis Sr. has hidden away. Domovoi "Dom" Butler, his loyal bodyguard, reveals a secret library filled with documentation that proves the existence of magical beings, a legacy of the Fowl family.
Meanwhile, in the underground world of Haven City, the realm of fairies, Mulch, a comically oversized dwarf and thief, gets intercepted by Holly Short, a reconnaissance officer with the Lower Elements Police (LEPrecon), leading to his imprisonment. Tasked with locating the Aculos, which is considered the fairies' most vital resource, Commander Julius Root dispatches his team. Foaly, the centaur technical advisor, identifies an unauthorized entity making its way to the surface. Despite the loss of her father, Beechwood Short, who perished while attempting to steal the Aculos, Holly takes to the skies to investigate. Her resolve strengthens when she intervenes during a rogue troll's attack on a human wedding, utilizing a "time freeze" to eliminate the threat and erase the humans' memory of the event.
As Dom's niece Juliet arrives at Fowl Manor, a series of revelations unfold. Through his father’s journal, Artemis learns that Beechwood had previously taken the Aculos to Artemis Sr. in an effort to safeguard it from the hooded figure, who turns out to be Opal Koboi—a vengeful fairy intent on annihilating humanity. Determined to fulfill his mission, Artemis sends Dom on a stakeout at the Hill of Tara. Holly, intent on avenging her father’s tarnished legacy, disobeys direct orders and flies to the same hill, where she stumbles upon Beechwood's ID tag but is swiftly captured by Dom and imprisoned within Fowl Manor's walls.
As the LEPrecon forces under Commander Root begin sealing off Fowl Manor using a time freeze, Artemis and Dom bravely counteract their efforts using Holly's advanced equipment. Artemis takes a stand, demanding the return of the Aculos in exchange for Holly's freedom while declaring a ban on fairies entering his abode as long as he lives. Bound by fairy regulations, Root negotiates with Mulch to break out of prison, proposing a shortened sentence in return for helping them infiltrate Fowl Manor. As Mulch digs his way into the manor and gains access to Artemis Sr.'s secured safe, the frantic search for the Aculos intensifies. In a daring move, Artemis frees Holly and pleads for her assistance.
In a shocking twist, Lieutenant Briar Cudgeon, a traitor working for Koboi, seizes control of the LEPrecon unit and sets a captured troll loose within the manor, obstructing all forms of magic. Mulch swallows the Aculos just as Artemis, Holly, Juliet, and Dom narrowly escape the rampaging troll. In a tragic turn of events, Dom sacrifices himself to save Artemis from the rampaging troll, leading to a dramatic confrontation where Holly’s fellow officers go against protocol and restore her magic, allowing her to revive Dom.
As Mulch and the LEPrecon team flee just before the time freeze collapses, Artemis resolutely holds onto the Aculos, refusing to hand it over to Koboi. In a stroke of hope, Holly agrees to employ its powers to save Artemis Sr. As Koboi threatens Artemis Sr., Holly bravely calls him to Fowl Manor. During this emotional reunion, Artemis Sr. reveals how Holly’s father sacrificed himself to guard the Aculos and provides her with a list of Koboi's accomplices. Holly vows to return the Aculos to Haven City, where a now-reinstated Root orders her to look into each name on the list.
In a final twist, Artemis dares Koboi, declaring his intent to pursue her. Meanwhile, Mulch’s interrogator presents him with an offer of freedom in exchange for assisting in capturing Artemis Sr. However, Mulch cleverly divulges that Artemis orchestrated his own arrest to validate the existence of magic to the authorities, confirming the world of magic exists on camera. As the interrogator calls for reinforcements, the Fowls’ helicopter descends to rescue Mulch, who, alongside Holly, makes a hasty exit into the sky.
