At Fowl Manor, Artemis is pleased with the discussion that he had with Root aboard the whaler. He needs the fairies to take him seriously in order for his plan to work. Artemis can see Holly in her holding cell in the basement, head in her hands. He experiences a twinge of misgiving, seeing her in obvious discomfort. He turns off his computer, intending to go talk with Holly. However, at that moment, Juliet bursts through the doors of his study and tells him that his mother is saying that Artemis Fowl Senior has returned. Artemis hesitates, knowing that his plan is time-sensitive, but eventually decides to go to his mother. When he enters his mother's room, however, it is immediately clear that his father's return is merely a delusion. She confuses Artemis for her own grandfather. She is dressed in her wedding dress, and in front of her, she has stuffed one of his father's old suits with tissue paper, and a pillowcase with a drawn-on face serves as his head. Artemis is upset at the scene in front of him, and he leaves her in her room.
Meanwhile, in her holding cell, Holly is trying stealthily to get at the object that is stuck in her boot without the cameras seeing. Eventually, she is able to release it and sees to her great pleasure that it is an acorn. This means that all she needs is a small patch of dirt, and her powers will be restored to her. However, the floor of her holding cell is thick concrete. She can tell that her cell was recently built—the concrete is still damp in some places. While she is examining her cell, Artemis startles her. He tells her to take a seat, and she is forced to obey. He calls her by her name, which surprises Holly, since her name-tag is written in Gnommish. Artemis informs her that he is fluent in Gnommish, and Holly tells him that what he has done—bringing together the human and fairy worlds—could have disastrous consequences for them all. Artemis does not seem fazed by those consequences, however.
Holly asks Artemis what his ultimate goal is, and he tells her he wants gold. Holly calls him a mere thief, to which Artemis takes slight offense. He informs her that he is the world's first cross-species thief, but Holly corrects him. The Mud People have been stealing from the People for millennia, which is why they are forced to live underground. Artemis tells her that he will be the first person to ever separate a fairy from their gold, which causes Holly to laugh. She thinks he believes in the gold-under-the-rainbow nonsense. However, always a step ahead, Artemis tells her that in fact he knows about the hostage fund. He tells her that Holly herself revealed its existence to him after he administered a truth serum (this is not true—Artemis lies to Holly so that she doesn't know that he has a copy of the Book). He lies to Holly a second time, telling her that she has been in Fowl Manor for three days, when in fact she has been there merely an hour. Artemis feels a bit of guilt as he sees how his lies affect the fairy in front of him, but this feeling does not derail his plans in any way.
Back at Ops, Root asks Foaly if he has any updates on the situation. Foaly tells Root that he found a ten-gigabyte file on the Fowl family, who have apparently been working on the wrong side of the law for generations. Foaly tells Root the location of Fowl Manor, and it is close enough to their current location that there is hope they might be able to clean this mess up before the light of day. Root and the Retrieval Squad take off towards the Fowl Manor, flying in a V goose formation. Outside the manor's bounds, Lieutenant Cudgeon—the leader of the Retrieval Squad—approaches Root and suggests that they simply blast the manor with a blue rinse. Root tells him that it is not worth the loss of Holly's life. Inside the Manor, Butler is watching the monitors, and Artemis asks him if he has seen anything. Artemis tells him to check the specialized cinecamera which processes images faster than the human eye can. Suddenly, Butler and Artemis can see twelve black-clad figures standing outside Fowl Manor. Artemis puts Holly's modified helmet on Butler's head and they discover that one of the helmet's visibility functions counteracts the shields that the fairies outside are using. Butler makes his way outside, where he easily takes down the twelve members of the Retrieval Squad. Butler grabs one of the officers and tells him to go back to base with a warning: if any more officers were to approach the manor, they will be picked off one by one with a sniper. He also allows the fairies to remove their injured. He then tells the officer that he wants them to send in a negotiator to talk to Artemis.
Meanwhile, Holly is trying to break through the concrete floor of her cell by banging her metal bed frame against it over and over again. Juliet enters, demanding to know what she is doing, and Holly tells her that she is hungry. Upstairs, Artemis is watching his mother through his security cameras and sees that she is asleep, having taken a sleeping pill that Juliet gave her. This is a vital part of Artemis's plan. In response to the Retrieval Squad being taken out of commission, Commander Root orders Foaly to place a Time Stop over Fowl Manor. With the Time Stop, the fairies have bought themselves eight hours to complete the mission. Foaly is worried that Artemis wants them to use the Time Stop—a suspicion that reveals itself to be entirely correct—but Root dismisses his worries.
Root finds Foaly, who prepares him to enter the manor and negotiate with Artemis. Foaly does not outfit him in heavy armor; instead, as a sign of good faith, he merely gives Root a camera disguised as a contact lens and a tranquilizer dart disguised on his hand. Root approaches the manor, and Artemis opens the door to let him in. Root tries to convince Artemis to come outside, but Artemis quickly outsmarts him. Artemis gives Root permission to enter the manor and then leads him to a conference room where they can conduct their negotiation. Artemis reveals to Root that he knows about the Time Stop and about the blue rinse. He tells Root that his only demand is one ton of twenty-four-carat gold. Root says that they will not negotiate with him: either they release Holly, or they will be forced to blue rinse the manor. Artemis responds that they will, in fact, negotiate, because he knows how to escape the Time Stop. Root tells Artemis he will have to think about all of this and excuses himself. Back at Ops, the videotape from the negotiation is reviewed by behavioral experts, who decide that Artemis is not lying when he says that he knows how to escape the Time Stop. Root decides it's time to start breaking protocol if they want to gain the upper hand.
In Chapter 6, the LEP team has arrived at Fowl Manor and are trying to recover Holly by any means possible. Their first mode of action is to send in their most elite squad of officers, Retrieval One, but they are easily taken down by Butler. Artemis has equipped Butler with a pair of goggles which counteract the fairy shield and a pair of reflective sunglasses which counteract the mesmer. Retrieval One is caught off guard by the fact that their magic is no longer useful to them, and Butler easily takes them down.
In this chapter, for the first time, we see more humanity in Artemis's character. First, he surprisingly expresses similar sentiments as Root about the whaler from the previous chapter: "Artemis leaned back in the study's leather swivel chair, smiling over steepled fingers. Perfect. That little explosion should cure those fairies of their cavalier attitude. Plus there was one less whaler in the world. Artemis Fowl did not like whalers. There were less objectionable ways to produce oil by-products" (109). Additionally, Artemis experiences a bit of doubt now that he has Holly trapped in his manor. As a reminder, Holly has lost her magical abilities and she has entered the Fowl Manor (though against her will) without an invitation. This means that she is forced to obey with whatever commands Artemis gives her. As Artemis watches her from a monitor in his study, he feels a twinge of guilt: "Artemis consulted the basement surveillance monitor. His captive was sitting on the cot now, head in hands. Artemis frowned. He hadn't expected the fairy to appear so . . . human. Until now, they had merely been quarry. Animals to be hunted. But now, seeing one like this, in obvious discomfort—it changed things" (109). He had expected the fairies that he comes into contact with to be extremely different from humans, and the visible similarities between them causes him discomfort. The fairies no longer belong in the realm of "animals" or "prey" in Artemis's mind and instead are inching towards the category of "people"—a potentially distressing prospect for someone who plans to exploit them. Artemis also feels slightly guilty about the mind games that he plays with Holly when they have their first conversation: "Better let the hostage believe that she had betrayed her own people. it would lower her morale, making her more susceptible to his mind games. Still, the ruse disturbed him. It was undeniably cruel. How far was he willing to go for this gold? He didn't know, and wouldn't until the time came" (117). Ultimately, seeing the way that Holly reacts disturbs Artemis. He was not expecting the fairies to hold so much resentment towards humans: "And it was that speechless quality that sent the doubt shooting through Artemis's brain. The fairy thought him so evil, she couldn't find the words" (118). It must be noted that Artemis's guilt does not throw a wrench in his plans nor does he try to make Holly feel any better about the situation she is in. He is forced to reckon with the fact that what he is doing is morally wrong, but that does not change his behavior in any significant way.
Importantly, when Holly warns Artemis that bringing the fairy and human worlds together would spell disaster for everyone, Artemis reveals an important aspect of his character: he is self-interested to a huge degree. He does not care about collective good over individual gain. "'You have no idea what you've done,'" Holly tells him. "'Bringing the worlds together like this could mean disaster for us all'" (115). This warning does not deter Artemis, who responds, "'I am not concerned with us all, just myself. And, believe me, I shall be perfectly fine'" (115). When Holly realizes that what Artemis is after is fairy gold, she accuses him of being "just a thief" (116). Artemis replies, however, that he won't be just a thief and instead will be "the world's first cross-species thief" (116). Again, Artemis's individualism supersedes everything else. He only cares about himself, his reputation, and his own personal gain. He does not have a response to Holly, however, when she informs him, "'Mud People have been stealing from us for millennia. Why do you think we live underground?'" (116). Here is an important difference between Holly and Artemis. Holly understands Artemis to be merely a part of the larger human race, which has collectively been committing atrocities for thousands of years. In Artemis's mind, however, he stands apart as an individual, and his species has little to do with it.
Root shares Holly's fears that bringing the fairies and the humans together will mean disaster. When considering what Artemis's motivations might be, he wonders if Artemis wants to expose the existence of the fairies to the rest of the human race: "It was even possible that this whole affair was media-oriented, and by tomorrow evening Captain Short's face would be on the cover of every publication on the planet. Root shuddered. That would spell the end of everything, unless the Mud People had learned to coexist with other species. And if history had taught any lessons it was that humans couldn't get along with anyone, even themselves" (120). Readers up to this point might see a slight irony beneath Root's words. It has already been established that Mud People pose a huge threat in the People's lives; however, it is also clear that the People often can't get along with themselves, either. For example, Holly passes Mulch Diggums as he is being locked up for committing crimes against his own people in Chapter 2. And in just a few chapters, Lieutenant Cudgeon will betray Commander Root and take over control of the rescue mission. In this way, perhaps Colfer is suggesting a gray area in the humans-are-bad/fairies-are-good binary. The individuals are what matter when it comes to either species, and they are often more similar to each other than they would like to admit. As Butler realizes in this chapter, the fairy officers exhibit the same behavior in the field as human officers: "Butler rolled his eyes. Different race, same macho clichés" (134).
A key bit of information that will be much more important in the final chapters of Artemis Fowl is the definition of the blue rise. As the narrator explains, "blue rinse was the slang term for the devastating biological bomb used on rare occasions by the force. The clever thing about a bio-bomb was that it destroyed only living tissue. The landscape was unchanged" (123). The LEP team will use the blue rinse as a last resort if Artemis refuses to release Holly in the long-term. If they were to release a blue rinse over Fowl Manor, everyone inside—Artemis, Butler, Juliet, Holly, and Angeline—would die. We will see how Artemis deals with this threat in the coming chapters.