Angeline Fowl contracts a debilitating disease, which Artemis II can not heal with magic. Artemis desperately contacts Captain Holly Short and N1, in hopes that they will be able to shed some new light on his mother's condition. They determine Angeline is suffering from Spelltropy, a fairy disease that is spread through the use of magic, and can only be cured by the brain fluid of the silky sifaka lemur of Madagascar. Unfortunately, the lemur is extinct, due to a ruthless deal Artemis made 8 years ago with a group called the Extinctionists. Foaly tells him that his mother will die without the cure. Artemis pleads for N˚1 to open up the time stream, allowing him to save the lemur, and thus his mother. Foaly argues against the idea, but due to Artemis' lying to Holly, saying that she infected Angeline with Spelltropy, Holly agrees to help Artemis immediately to make up for it, and Foaly has to give in.
They arrive nearly eight years earlier in Angeline's bedroom. Artemis assures Holly that Butler will quietly slip the lemur into the room (to avoid Angeline seeing it) and that they will simply be able to leave. Butler however, does not act according to Artemis' predictions. He tranquilizes the two, and imprisons them in the trunk of the Fowl Bentley. Artemis and Holly escape with the help of Mulch Diggums, a kleptomaniac dwarf that has partnered up with Artemis in the future. They save the lemur from Rathdown Park, but are forced to release it to young Artemis. They then get to the shuttleport in Tara, where Artemis tells Holly the truth about his mother's illness. They fly the shuttle to Fez in Morocco, where the younger Artemis is trading the lemur for a hundred thousand euros. The money is to go toward the Arctic expedition,so that Artemis can search for his missing father.
Artemis, Holly, and Mulch go to the rendezvous point where the younger Artemis is making the exchange. However, during their plan to rescue the lemur, Holly is caught by Butler. 10-year-old Artemis sells her to Damon Kronski to replace the escaped lemur, and she is put on "trial" by the Extinctionists. Naturally, Artemis saves her, but during the ensuing chaos, he falls in the execution pit himself. There he discovers that the "flames" were holograms, and meets his old nemesis Opal Koboi. He escapes, finds Holly, and flies back to Fowl Manor to return to the future. However, Opal follows them into the time stream, escaping to a time several weeks before Artemis's initial departure. She takes over Angeline's body and pretends that she is Artemis' mother. She reveals herself as Artemis is about to inject the fluid into her system, and tells him that she caused his mother's symptoms.
As Koboi gloats, Artemis reveals that he is in fact the Artemis from the past. The older Artemis then returns to the future to find young Artemis, Holly and N˚1 trapped and Butler mesmerized. When Butler is ordered by Koboi to take out the younger Artemis, he fights Koboi's mesmer and has a heart attack, causing the younger Artemis to have to revive him with a portable defibrillator. The older Artemis finds the real Opal and tranquilizes her. Opal recovers quickly and flees; however, realizing that Artemis and his forces have been significantly weakened in the battle, she returns. Artemis takes Jayjay (the silky sifaka lemur, given that name due to his resemblance to Julius Root) and flies away from the Manor grounds in a plane, luring Opal away. In the ensuing chase, Opal exhibits astonishing strength, pulverizing entire sections of the plane with her fists, eventually forcing Artemis to crash land on the coastline, which results in his collarbone being broken. Artemis escapes from the wreckage of the plane and runs to the shore, ascending a rope bridge and crossing over two large boulders. Opal relentlessly pursues him, eventually obtaining Jayjay, only to discover that it's not actually Jayjay, but Artemis' little brother's play-thing, Professor Primate. Artemis shoots the boulder which Opal is standing on and which is revealed to be the shell of a kraken that was unknown to anyone except Artemis himself. The shell explodes, and Opal is buried beneath the rubble. When a Lower Elements Police team search for her, they find she has disappeared. Artemis debriefs the others and finds that his mother knows everything that happened to her. The 10-year-old Artemis has his mind wiped and is sent back in time by N˚1(10-year-old Artemis has a spell in his eyes that will erase Butler's memory), but begins to remember something about fairies, creating a circular timeline.
Souce: Wikipedia