NOTE: This spoiler was submitted by Jeremy

The film starts with a swarm of reporters outside Fowl Manor. Artemis Fowl (Ferdia Shaw) is being pressed by reporters on questions regarding his father, reported to be a notorious criminal mastermind. Artemis’s associate Mulch Diggums (Josh Gad) is taken into custody.

Mulch is interrogated at an MI6 fort in London, where he tells his captors the full story of the Fowls, as well as a world of magic not known to humans. He begins by introducing Artemis living in his homeland of Ireland. While a clever boy, he acts out and must see a school psychologist, who asks Artemis if he is acting out due to his mother’s death or because his father is an alleged criminal. The boy walks out of the meeting.

Artemis enjoys being with his father, Artemis Sr (Colin Farrell), who told him countless stories of fairies, leprechauns, and other magical creatures. Artemis knows his father is going away, as he constantly does, but Artemis Sr promises that his work is coming to an end. He assures his son that he will still keep him safe. Artemis watches his dad depart on his helicopter, but not before Artemis Sr leaves him with a poem, “The Irish Blessing”.

The Fowls’ butler, Domovoi Butler (Nonso Anozie), receives a message that Artemis Sr’s boat arrived at its destination without him. Artemis sees a news report claiming that his father is responsible for a number of crimes scaling the globe that involve stealing priceless artifacts and antiquities. Dom drags Artemis away from the TV as the boy yells that it cannot be true that his father is a criminal. Artemis then gets a call from a mysterious figure named Opal Koboi (Hong Chau). She has kidnapped Artemis Sr and tells Artemis that he has three days to acquire an artifact known as the Aculos, or she will kill his father. Dom then takes Artemis to show him a secret room used by Artemis Sr and the generations before him. Dom shows Artemis a bunch of relics that the Fowls have collected, as well as notes detailing the world of the fairies. Artemis figures that he must find his father’s journal to see where he might find the Aculos. He realizes that the poem his father told him is a clue, and he finds a copy of “The Irish Blessing” to find that it is Artemis Sr’s journal. He wrote about how he and his partner Beechwood acquired the Aculos.

We go to the center of the earth, which is the location of Haven City, home of the fairies. They are also struggling to find the Aculos. Mulch is shown with a community of dwarves that he belongs to, despite not actually being a dwarf himself (although he insists he is), where he is sentenced to hard labor due to a number of crimes. He talks to Officer Holly Short (Lara McDonnell) to try and help him out, but she denies him. Meanwhile, Opal is able to free former fairy commander Briar Cudgeon (Josh McGuire) and reinstate him to his former position so that he can help her get Artemis and the Aculos.

Holly reports to her position at Lower Elements Police Reconnaissance (LEPRecon) where Commander Root (Judi Dench) addresses the other fairy officers about the situation regarding the Aculos. Holly asks Root if she can investigate her father’s disappearance at the Hill of Tara, but Root denies her request. However, Root still shows confidence in Holly’s abilities as an officer.

While Artemis continues his investigation, Dom gets his niece Juliet (Tamara Smart) to come help. Artemis also gets a lead to the Hill of Tara, but he needs a fairy to help him out since their language is encoded by a centaur technician named Foaly (Nikesh Patel). He gets a reading from the surface with ties to the Aculos, so Root sends Holly up on the mission. She is dropped off and flies near the location of a party. She encounters a gigantic troll attempting to eat a little girl. Holly saves the girl, but Root and Foaly establish a Time Freeze before any humans get hurt. Despite Root telling her not to use magic, Holly does so to treat the girl’s wounds. They get rid of the troll and wipe the humans’ minds before putting everything back to normal.

On her way back home, Holly decides to go by the Hill of Tara to clear her father’s name. Artemis and Dom go by the area in camouflage where they spot Holly walking nearby. She realizes she is being watched and tries to fly away, but Artemis and Dom shoot her down and capture her. Foaly tracks Holly’s location to Fowl Manor, and Root sends everyone out before their existence becomes known.

Holly wakes up in a cage set up by Artemis. He and Juliet are wearing sunglasses to prevent her from using her magic to control their minds. Root’s fairy officers head over to Fowl Manor to retrieve Holly, and Foaly sets the Time Freeze in place. The fairies swarm the manor, but Artemis and Dom fight them off using Holly’s confiscated weapon, and they manage to disrupt the Time Freeze. Root makes her way toward the house, and Artemis lets her inside. He tries to negotiate with Root to exchange Holly for the Aculos, despite not knowing that they don’t have it. Artemis goes to talk to Holly, where he learns that Beechwood Short was her father, and that both their fathers worked together, but Beechwood was framed as a traitor to the fairies. She explains that the Aculos can be used as a portal between worlds.

Opal talks to Artemis Sr about her motivation. Since she thinks humans and fairies cannot coexist, she wants to use the Aculos to unleash her army and rule over both worlds.

Root calls upon Mulch to be released and has him dig his way into Fowl Manor. He manages to find the Aculos hidden behind a portrait of Artemis Sr inside a safe. Artemis then frees Holly once they realize Mulch is in there. They try to hide the Aculos from the other fairies, but they already saw it through Mulch’s eye camera. Cudgeon reports to Opal that the Aculos has been found, so she orders him to intervene. He relieves Root of duty and releases the captured troll into the house, effectively jamming the magic in the house. Cudgeon says he gave the troll a mixture that made it stronger and angrier and will use it to get the Aculos.

Artemis teams up with Holly, Dom, Juliet, and Mulch to secure the Aculos and fight the troll. Mulch swallows the Aculos while the others go about fighting off the beast. Meanwhile, the Time Freeze continues to grow more and more unstable, causing many fairies to get thrown around. The heroes then manage to trap the troll by tangling it in a chandelier. It almost collapses on top of Artemis until Dom pushes him out of the way, which mortally wounds him. Holly convinces the other fairies to help, and they turn against Cudgeon to let her use her magic to revive Dom. When she realizes her plan has failed, Opal attempts to kill Artemis Sr by trapping him in dark magic. Artemis gives the Aculos to Holly since no human can wield it, and Holly uses it to bring Artemis Sr back, causing Opal to scream in defeat. Artemis Sr embraces his son and tells Holly that her father gave his life to protect the Aculos. He also gives her a list of Opal’s accomplices.

Holly brings the Aculos to Haven City, where Root keeps it safe and then launches an investigation into Opal’s cohorts. Artemis calls Opal personally and promises he will go after her.

Mulch finishes his interrogation and is offered freedom for his services, but Artemis and his father, plus Holly, arrive in their helicopter to get him out. They then fly off toward another adventure.

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Artemis Fowl's father goes missing just after he is declared to be a master criminal. The family's butler, Dom, reveals to Artemis that his father and other past generations of Fowls have known about the existence of the magical world beneath them.

A rogue fairy named Opal Koboi has kidnapped Artemis Sr and demands an artifact called the Aculos, which will grant her control of both the human and fairy world. A fairy officer named Holly Short is caught by Artemis after she tries to investigate a case surrounding her late father. He and Artemis Sr worked together to protect the Aculos from the forces of evil, but her father was branded a traitor to the fairies. Commander Root then sends other fairies to get Holly back, unaware that one of her men is a spy working for Opal.

Root sends dwarf Mulch Diggums into Fowl Manor to help out. He manages to find the Aculos, but Opal's spy sends a troll in there to get the heroes. They defeat the troll and use the Aculos to retrieve Artemis Sr from Opal's clutches.

Holly returns the Aculos to the fairy world for safety, and she teams up with Artemis and his father, plus Mulch, to go off on other adventures.