Artemis Fowl and the Atlantis Complex (formerly Artemis Fowl: The Atlantis Complex) is the seventh book in the Artemis Fowl series by Eoin Colfer.
At the beginning of the novel, Artemis Fowl meets with Captain Holly Short, Foaly, and Commander Vinyaya in Iceland. There Artemis reveals that he has created and invested in a new idea to save the world. He has created a small nanofiber flake that (when created in sufficient numbers) acts as imitation snow. His plan is to coat all of the glaciers in the world with this compound so that the new reflective coating can save the icebergs from melting. As they talked, both Holly and Foaly realize that Artemis's behavior is strange; he constantly counts his words, and asks the fairies to arrange their seating by height. They conclude that Artemis has contracted the Atlantis Complex, a mental disorder common in criminals. The symptoms of the disease are similar to OCD, in addition, those who have contracted it may also experience paranoia, and multiple personality disorder. (On a side note, the disease was first diagnosed by one Dr. E. Dypess. This is much like Artemis' pseudonym in The Lost Colony, Dr. C. Niall DeMencha, whom he talked about with his fellow child genius Minerva and whose name forms the phrase, "senile dementia.") As a result, Artemis begins to arrange his life around the number five (such as arranging his sentences into increments of five and avoiding the number four). He doesn't trust anyone, and as later displayed, he has an alter ego: Orion. While Artemis Fowl is displaying the invention, which he has dubbed the Ice Cube, an unknown Lower Elements Police space probe enters the atmosphere above them. When the probe impacts the shuttle the LEP arrive in, Commander Vinyaya instantly dies trying to save her men. Holly and Foaly are safe, but Artemis is standing right in the way of the so-called "scientific probe." Artemis actually believes that the probe is one of his delusions, and that he has to face his fears. Stranded on a rooftop, Holly cannot do anything to save him. She ends up having to shoot out the ground underneath Artemis to get him out of the way. Meanwhile, having received an urgent text message from his sister, Juliet, Butler travels to Cancun. Once he gets there, he finds out that Artemis fabricated the message just to get him out of the way due to mistrust. When he arrives, the fictional danger turns out to be real when a fairy appears on the jumbotron system and urges the fans to attack him and his sister. Butler manages to hold them off until Juliet disables the system, returning the people back to normal. As the reuinted siblings trie to travel away, they are waylayed by a group of renegade dwarves who plan to mind wipe them of all their fairy knowledge (and everything else). But the two are saved by Mulch Diggums, who joined the dwarves under a false idenity.
It is then revealed that Turnball Root was behind the havoc. He has figured out how to create a small spark of magic, despite having lost his, and used this skill to brand a control rune onto one of the guards, who provided him with all he needed to enact his plan. Root and his crew of n'er-do-wells escape the prison shuttle and fake their deaths when a rogue probe crushes the prison transport.At the same time, after Holly shoots Artemis with a jolt of electricity and the impact forces him out of the way, when the group comes together again, they find that Artemis is no longer himself. He has reverted to Orion, a carefree, optimistic alter ego who openly claims his love for Holly and calls Foaly a noble steed (much to the centaur's displeasure). Orion is obviously unaffected by the weight of the situation, and is also completely incapable of scheming, a trait which is unfortunately most vital seeing the group's status.
The group locate an escape shuttle and use it to follow the probe, which is drilling into the ice on a direct course to the city of Atlantis. The oxygen tank ruptures, air is running out, and Holly is forced to knock out both Orion and Foaly to conserve oxygen long enough to get a warning out. Ironically, the zap causes Orion to revert back to Artemis. They are then contacted by Commander Kelp, who forbids them from investigating any further. However, he implies they should look into the situation. Mulch, Butler, and Juliet then meet up and join Artemis, Holly, and Foaly. Turnball travels to Venice. He then finds his human wife and concocts a plan to make her young again. After tangling with a giant squid, Artemis finds a computer core. The fairies follow the trail back to Venice, and make plans to confront Turnball. But their sub is intercepted and they are captured. Turnball brands Artemis and Holly with his control runes and enacts his plan to kidnap a certain demon warlock to restore his human wife's youth.
In Atlantis, No. 1 aids in the healing of the injured, when Holly, who is under Turnball's control, convinces him to follow her onto a modified ambulance ship to help an "injured" Artemis. A fight ensues when the now freed LEP and humans (who manage to break free thanks to Mulch) encounter the remaining members of Turnball's group. Things look grim when Juliet and Butler lose and all that is left is an unconscious Artemis, a slightly crispy Mulch, and Foaly. The tables are turned when it is revealed that despite Artemis being under Turnball's control, Orion is not. The genius's alter ego manages to knock Holly out despite her stating that Artemis would never shoot her. Turnball has one last trump card: he has rigged the ship to explode. Turnball's wife, who is now very old, finds out about Turnball's scheme to extend her life. She then tells him she has lived a long life and wants to go on one final journey. She flies the ship away with Turnball by her side. The ambulance explodes, killing them instantly, and allowing the humans and fairies to escape.
Artemis later regains consciousness (thanks to a bit of No.1's magic that puts him temporarily in control), but is still under the influence of the Atlantis Complex. Butler calls Angeline and tells her of her son's condition. When she expresses that she wants to be by his side, Butler informs her of a squad of LEPrecon fairies that are already en route to transport her to Atlantis, where Artemis will undergo therapy to let go of his guilt for the crimes he has committed over his prosperous career.