At the beginning of Chapter 5, Commander Root and the rest of the Retrieval team return underground. Root goes to Ops to talk to Foaly, who tells them that it appears that Holly has been kidnapped by two humans. They overhear the audio feed from Holly's helmet, and Root gets progressively more concerned about Holly's wellbeing. He is shocked that two humans seem to know so much about the fairy world. Root goes into command mode and tells Foaly to get the Retrieval squad out of their beds. In an unprecedented move, he puts himself back in action for this mission. He tells Foaly to get a pod ready—he is going to the surface as soon as possible. Foaly follows Root's commands with little argument, because he is worried about Holly, who is one of the only friends he has.
Meanwhile, Artemis, Butler, and Holly are in Artemis's van. Artemis is inspecting the fairy technology that he took out of Holly's helmet, which he finds impressive. He discovers a locator among the technology, and suddenly gets an idea. He tells Butler to make his way towards the docks, where there is an abandoned Japanese whaler. At the same time, Root speeds through the process to reactivate himself in the field and puts on his old uniform. He ignores the fact that it is slightly snug around his midsection. The nearest chute to Holly's location is the one that leads to Tara, a fairy hotspot that will be crammed with tourists. Root has no choice but to use that location, as the moon will be in the sky for only two more hours, and the fairies cannot be aboveground during the day. Foaly straps Commander Root into a pod, and Root is a bit nervous about having to travel in a pod again. However, the trip goes smoothly.
As Root makes his way to the surface, Artemis is quickly making alterations to Holly's locator. Even though fairy technology and human technology are vastly different, Artemis eventually is able to open the piece of technology in order to see its inner mechanisms. Artemis is able to input a small camera in the locator and clumsily closes it back up with glue. Butler and Artemis make it to the docks, and Artemis asks Butler to create a diversion. In order to do so, Butler picks a fight with a group of six dockworkers who are smoking cigarettes. He insults them, causing them to try to team up against him in a physical fight. They are no match for Butler's training, however. He easily defeats the six men, causing a large enough of a diversion that the policemen watching the dock approach. Butler escapes before they can apprehend him. Butler makes it back to the car and Artemis is already there, waiting for him.
When Root makes it to Tara, he finds a terminal crammed with tourists who are unhappy that the gate has been closed. When they ask him about it, however, he tells them there is a critical situation aboveground and tells them all to sit down. Commander Root asks to see whoever is in charge of the terminal, and an elf/goblin hybrid comes up to him. Root asks to be let out of the terminal and says he does not want to be bothered by customs and immigration. He then tells the elf/goblin hybrid to completely evacuate the terminal. Back at Fowl manor, Holly is waking up. Juliet greets her and tells her that she is in Fowl Manor as a prisoner. Holly shudders when she hears Artemis's name. She warns Juliet that her People will come for her, and that they have no idea what they have done. This threat does not faze Juliet, much to Holly's chagrin. Holly tries to convince Juliet to take off her reflective glasses so she can use the mesmer, but Artemis already warned Juliet not to remove them under any circumstances. Holly then threatens to fight Juliet, but Juliet merely laughs at her. She tells Holly that she knows that Holly is bound to do everything that the humans tell her to do as long as she is in their dwelling. She also warns Holly that she is a highly capable fighter and has been looking for someone to practice her wrestling moves on.
Meanwhile, Commander Root is tracking down Holly's locator. Root tells Foaly that his map of Dublin is outdated, and Foaly takes two minutes to update it. When it is updated, Foaly sees that the locator is somewhere offshore, seemingly aboard a ship. When Root makes it to the deck, Foaly tells him that his technology won't help him locate Holly. Root is on his own. Root is disgusted by the whaler—many whales have been slaughtered aboard the ship so that their blubber could be converted to human commodities. Root makes his way towards Holly's locator. He finally finds it belowdeck in an abandoned room. Artemis's voice greets him when he gets inside. However, Artemis is not in the room—the voice is tinny and artificial. Root discovers that Artemis is watching him from a camera, and Holly is not in the ship—she is, in fact, far away. Artemis has rigged the room with explosives, and Root is barely able to get out in time to escape the blast.
In Chapter 5, Commander Root and Foaly discover that Holly has been kidnapped, and they immediately leap into action. Meanwhile, Artemis takes Holly back to Fowl Manor, but he and Butler first stop at the Dublin docks to create a diversion. In order to do so, Artemis must modify Holly's field locator (the device that tells the LEP headquarters where Holly is at all times). This requires him to work with fairy technology, which, by its nature, is very different from the human technology Artemis is used to. His first step is to open up Holly's field locator in order to see how it works: "Artemis was performing a little field surgery on the fairy locator. It was no mean feat to alter some of the dimensions without destroying the mechanisms. The technologies were most definitely incompatible. Imagine trying to perform open-heart surgery with a sledgehammer" (86). Despite the fact that Artemis is disadvantaged, he quickly finds his way: "The circuitry was minute. And not a sign of a solder bead. They must use another form of binder. Perhaps if he had time the principles of this device could be unraveled, but for now he would have to improvise. He would have to rely on the inattention of others. And if the People were anything like humans, they saw what they wanted to see" (87). Like the process by which he is able to translate the book, Artemis finally finds success with the fairy technology by using his common sense and believing that fairy logic is like human logic. He is able to modify Holly's locator enough that Root follows it to an abandoned whaler which allows Artemis, Holly, and Butler to arrive at Fowl Manor without incident.
The abandoned whaler is a source of disdain for Commander Root. A whaler is a large ship that is used to hunt whales so that they can be sold for their blubber. Whaling enterprises have led to the death of countless whales, putting their existence at risk on a global scale. Artemis lures Commander Root to the ship, where the commander is revolted at what he finds. Root describes what he finds: "It was an ugly craft, this one. The smell of death and pain lingered in the blood-swabbed decks. Many noble creatures had died there, died and been dissected for a few bars of soap and some heating oil. Root shook his head. Humans were such barbarians" (102). In contrast to the scene of death that prevails on the whaler, Root demonstrates the different kind of relationship that fairies have with animals while aboard the ship. For example, when he comes face-to-face with a rat, he does not kill it: "Still no sign of life—human or fairy. Plenty of animal. Mostly rodents. And when you're just topping three feet in height yourself, a good-sized rat can be a real threat, especially since rats are one of the few breeds that can see straight through a fairy shield. Root unstrapped his blaster and set it to level three, or medium rare, as the elves in the locker room called it. He sent one of the rats scurrying away with a smoking behind as a warning to the rest. Nothing fatal, just enough to teach him not to look sideways at a fairy in a hurry again" (103-4). Commander Root demonstrates a different way of relating to animals that does not lead to extermination. Instead, he warns the rats aboard the whaler, so that they are only slightly harmed but know to stay out of his way.
One character who we get to know better throughout Chapter 5 is Commander Root. He is a grumpy, centuries-old elf who cares about Holly despite his toughened exterior. As soon as it is clear that Holly has been kidnapped, he places himself in the field even though he has been taken out of combat. This is unprecedented, but they are in an unprecedented situation and Holly is in extreme danger. There are moments throughout Chapter 5 which give us a humorous look into Root's character. For example, when he rides a pod aboveground, he is uncharacteristically shaken: "Root emerged shaking from the pod. He didn't remember it being like this in his time. Although, truth be told, it had probably been an awful lot worse. Back in the shillelagh days, there were no fancy polymer harnesses, no auto thrusters, and certainly no external monitors. It was just gut instinct and a touch of enchantment. In some ways, Root preferred it like that. Science was taking the magic out of everything" (92). Root is an old-timer who distrusts the technological advancements that fairy society has made in recent years. Despite this, he is intelligent and proficient at his job. When he is aboard the whaler, fairy technology can no longer help him, but he is still able to inspect it and get out alive: "Root was on his own. Truth be told, that was the way he liked it. No science. No uppity centaur whinnying in his ear. Just a fairy, his wits, and maybe a touch of magic" (101). Root's experiences when trying to hunt down Holly speak to a major conflict in Artemis Fowl: that between modernity and tradition. In many ways, Root emblematizes the traditional way of life: he is in tune with nature and relies on his own intuition to get through challenges. Artemis, his rival throughout the novel, is his opposite. He is young, intelligent, and extremely dependent on the most advanced human technology, which he deftly uses to his advantage. As these two minds face off in this chapter and the ones to come, it is unclear who will come out the victor. They are each others' equal match. In this way, Root is Artemis's foil. In literature, foils are characters that embody opposite characteristics in such a way to emphasize the differences between them.