The Lost Colony is the fifth book in the Artemis Fowl series. Artemis Fowl is the boy genius that discovered a fairy world that is unknown to the mortal world. Artemis, through his knowledge of the fairy world and his relationship with LEP Recon Agent Holly Short, has experienced several adventures. Artemis is an excellent example of an anti-hero. Most of his exploits, especially at the beginning of the series, are selfish and his actions are self-serving; however, he tends to be cornered into doing the right thing and saving the world or his friends.
This adventure begins in Spain, where Artemis and his bodyguard/servant/friend Butler are waiting to meet a demon. When they give up and move to leave, Artemis suddenly realizes that the demon is coming but it is in the middle of the street. He shakes hands with the creature and is whisked off through time. Butler, who is wearing silver, is able to drag Artemis back from his adventure.
Meanwhile, Holly Short, who was dismissed from the LEP in an earlier book, is now an elfin private investigator with Mulch Diggums. She is brought to the secret headquarters of Section Eight. This branch of the LEP focuses most of its efforts on monitoring demons. Artemis' activity with the Demon has alerted this specialized group and Holly has been brought in because she is an expert on the human troublemaker. She is sent to figure out what Artemis knows.
On Hybras, a demon island that was locked away in time, an Imp named No 1 is an outcast because he has not Warped (become an adult demon). He is strange because unlike his fellow demons, he does not want revenge on the human world. No. 1 suspects that he might be a demon warlock after he turns a wooden skewer into a stone. Leon Abbot, a demon war hero, "mesmers" (hypnotizes) No1 into jumping into a volcano. This will allow him to cast a time spell and return to the human world.
At an Opera House, Holly approaches Artemis and Butler. When No.1 appears, he is shot with a tranquilizer dart by a strange blonde woman by the name of Minerva Paradizo and her mercenary, Billy Kong. Holly chases after the duo and the unconscious imp. No.1 tells Minerva about demon culture. Minerva reveals that she plans to put all the demons in a zoo. Holly is captured attempting a rescue of No.1. While Artemis distracts Minerva, Holly and No.1 escape as Folly (the centurion LEP technical specialist) uses a bug to destroy all of Minerva's research.
Billy Kong decides that he needs to destroy all of the demons. He takes Minerva hostage and makes a deal with Artemis to trade her for No.1. Billy Kong's plan is to strap a bomb on No.1 and send him back to Hybras. (He is being anchored to the real world by a silver bullet.) After the trade, No.1 drops the bullet and escapes by dematerializing to Holly who secures him to this world with a silver bracelet.
They then travel to the art gallery where a famous statue is in fact demon warlocks that were frozen in stone when casting a time spell. Artemis releases the demons from the stone, but only one Qwan has survived. Kong attacks and the bomb is handcuffed to Holly. Artemis takes off No.1's silver bracelet and he, No.1, Holly, and Qwan are transported to Hybras. Minerva and Butler have Billy Kong arrested.
Artemis and the others are taken to Abbot, who has crowned himself King. Artemis reveals that he intends to use the bomb to give the energy needed to break the time spell. Qwan reveals that five magical beings are necessary to complete the spell- they only have three. When they are taken to Abbot, Artemis reveals that he has the ability to use magic. With Abbot they have the five magical beings needed to release the time spell. Abbot has the demons attack and Holly is killed. In order to bring her back to life, Artemis taps into the disintegrating time spell's energy. Qweffor, Qwan's apprentice takes over Abbot's body. His spirit has been locked in Abbot's head. With his magic, they are able to end the time spell's lock on Hybras.
Back in the human world, they find that it is three years later. Holly and Artemis have also exchanged one eye each. The world has significantly changed, including the fact that Artemis has twin brothers.