Part 1: Revelations
The story picks up following the events of Freefall. In the world with its own sun in the centre of the Earth, the Rebecca twins had dived into a pool in order to escape an explosion set off by Will and Elliott, and eventually are able to survive by breathing air they find trapped in the roof of some underground workings. Chester and Martha return Topsoil, where Chester is inevitably very eager to contact his parents, but Martha won't permit this. She dotes obsessively on the boy, seeing him as a substitute for her dead son. This frightens Chester, who begins to make a plan to run away from her, but in the event doesn't dare put this into practice. Meanwhile, back in the centre of the planet, the Rebeccas come across a modern metropolis, with helicopters and other vehicles, including cars resembling Volkswagens. The point of interest flips back to Chester, when they are walking through the night. Suddenly, Martha grabs him, and Chester panics, going as far as to hit her. When he demands an explanation, she claims she was shielding him from a Bright. Under the surface, Rebecca Two sees a Limiter flare, and then signals back by blowing up a gas tank. The Rebeccas then continue to march toward the city.
The story returns to Chester, who wakes up, finding Martha, who just killed a bird. He and Martha eat the bird. The Rebeccas find the city, and realise it is well maintained and populated. They frighten a small amount of people, and that results in the arrival of the local army. The people of the city are from a expeditionary force that arrived during World War II. The Limiter forces arrive shortly, and a short staredown occurs, and after a Limiter medic begins to operate on the wounded Rebecca. The other Rebecca and the Limiter General begin to talk about their identity. During the second World War, the Styx were allies of the Third Reich. The officer of the squad informs the other two that they are "New Germanians". The officer takes Rebecca and the Limiter General to meet the Chancellor of New Germania. Back Topsoil, Chester's food that Martha is feeding him makes him sick. They enter a small cottage that is unattended. They discover that it is well kept, and has various foods. Chester eats some cold beans, and takes a shower. He then returns to the kitchen, after getting some new clothes. He begins to call his parents, when he is hit in the back of the head and knocked out. The story shifts to Drake, who wakes up in a room he does not recognize. He heads to a window, and realises that he is still Topsoil. He is then greeted by his savior, a retired Limiter named Edward James Green, who believes that the Styx are taking unnecessary measures with their goal of reclaiming Topsoil. He also reveals himself to be Elliott's father. They then discuss various aspects of the Limiter, who is coined "Eddie" by Drake. After finishing, they head for a keypad-locked cellar. The story then flips to Will, Dr. Burrows, and Elliott. They discover a group of skulls, which prove that there are native inhabitants. Dr. Burrows also claims to have seen a Stuka. Elliott prepared some early warning systems in case of Limiters or other people. She also prepares a hidaway for them to run to in case of danger, and shows Will the ancient passage the Rebeccas used to enter the inner world, also finding evidence that Limiters have been there recently. Meanwhile, Eddie and Drake enter the cellar, and Drake discovers an area akin to a briefing room. He discovers various Styx elements, including a Dark Light and the device used to incapacitate him in the Commons. Eddie then leaves Drake, giving him keys to the warehouse and the apartment. Back underground, Will and Elliott find free time together, but are soon interrupted by Dr. Burrows, who is investigating the pyramid area, against precaution by Will and Elliott. Back Topsoil, Chester is held hostage by Martha, and is fed a mystery meat. Drake and Eddie eventually find him, but he is revolted when he finds he was eating meat from dead mailmen, whom Martha killed. Back in the Colony, Mrs. Burrows is kept alive by the Second Officer, but her presence in the house begins to make his family very unpopular. She slowly regains motor control of her body, but her sight has been badly impaired and she compensates this by utilising an olfactory super-sense that she finds that she has developed. The family begins to consider ways of killing her. Back Topsoil, Chester meets Eddie, and wants to return to his parents. The Prime Minister, meanwhile, is Dark Lit. The Rebeccas also convince the Chancellor of New Germania to let them use the helicopters to search for Will, Dr. Burrows and Elliott.
Part 2: Contact
The Rebeccas find that Tom Cox is still alive, and with them. The Chancellor then assigns Colonel Bismarck to assist them. They board helicopters, and head for the pyramids. They find Will and Dr. Burrows, and capture them. Elliott watches the scene from high in one of the giant trees of the jungle, and before Cox manages to slice off Will's fingers at the behest of the Rebeccas, she shoots and kills him. The Rebeccas are angered by this, and the shoot Dr. Burrows as retaliation. They then demand that Elliott surrenders and hands over the Dominion virus, as they found the broken phial containing the vaccine. Elliott comes up with a plan, and approaches with a suicide bomber kit. She then forces the Rebeccas to let them go, in exchange for the virus. They agree, and the exchange is carried out just as Will and Elliott are leaving on a helicopter with Colonel Bismarck. Meanwhile, Eddie informs Drake that the Styx obtain their viruses from "Plague Snails" that live in the eternal city. Chester's attempt to contact his parents goes horribly wrong as the Styx have brainwashed them to not recognize him and to call one of their agents if he appears.
Part 3: Restitution
Colonel Bismark cannot land Will and Elliott at their supply cache in the jungle due to one of the inner world's frequent storms, and lands them as close to the location as possible. Once landed, Will confronts Elliott, asking her why she gave the Styx the virus. She tells him that she has the vaccine that she drank it before breaking the phiall. Meanwhile, Chester and Drake deprogram Chester's parents, who've been brainwashed by the Styx. Eddie and Drake also inspect a portal into the underworld, in preparation for an underground operation. Also, the Rebecca Twins and their Limiters take the New Germanians assigned to support them prisoner as part of their plan to take over New Germania. As they brainwash the captives, it becomes evident that one of the Rebecca twins is infatuated with the New Germanian officer that they first met when they arrived at the city. Will and Elliott retrieve their weapons and supplies and start making their way through the ancient passage to the fallout shelter. In the Colony, the Old Styx tells the Second Officer that he should be prepared for the Styx to take Mrs. Burrows to the Scientists to be examined to see how she resisted the Styx's Dark Light battery for so long.
Part 4 : On The Offensive
Drake and Eddie leave the warehouse to place pesticides that will annihilate the plague snails in the Eternal City, leaving Chester behind to watch movies. Meanwhile, the Second Officer's family rejoices when the supposedly comatose Mrs. Burrows is taken to have her brain examined by the Scientists. Colly, the family's Hunter that Mrs. Burrows befriended, hisses at them, and they cannot understand why she is upset.Will and Elliot make their way to the fallout shelter, but are stranded there because Chester and Martha took the only intact boat. At the warehouse, Chester calls his dad to tell him that their part in Drake's plan is ready, but he finds that his Mother has disappeared. He tells him that the plan has not changed, and the last place he wants to be is at the hotel if Emily Rawls has indeed fallen under the power of the Styx. Drake and Eddie place the charges and detonate them, releasing a cloud of pesticide that will destroy the plaque snails. Chester and Jeff Rawls make their way to the portal, and Jeff goes to the warehouse after Chester has found the portal and begun to unpack the equipment Drake had him to bring with him: two bergens, some firearms, and a noddy suit After fighting their way through a Styx patrol, Drake attacks Eddie, knocking him unconscious. He did this partly because while Eddie was working for the Styx, he tortured and killed a close friend of Drake's, and then lied about the incident to Drake; but mostly because Eddie would not consent to what Drake and Chester were about to do next. Meanwhile, the Rebecca Twins finish their takeover of New Germania. Drake and Chester make their way through the Labyrinth, and attack the South Cavern's air supply, piping in nerve gas (which was in one of the Bergens that Chester brought down into the underworld) to incapacitate as many colonists as possible, so they will not interfere in the next part of the mission. Meanwhile, the Second Officer and Colly go to the Laboratories to make a last visit to Mrs. Burrows. Drake and Chester arrive at the Laboratories, tranquilizing any colonists the nerve gas didn't incapacitate and plant explosives (which were in the other bergen) in the North Block, which specializes in weapons and biological warfare research. Drake and Chester search the building for any Topsoilers being captive in there. Chester finds the Second Officer and fights with him, as Chester believes the Second Officer was complicit in Chester's torture, and the Second Officer has a grudge against Will and his friends because Will knocked him unconscious during the unsuccessful attempt to rescue Chester from the Hold. Mrs. Burrows stops pretending to be unconscious to break up the fight, but Eddie (now recovered) locks them in the operating theater. Eddie then paralyses Drake with the Dark Light training Eddie gave him while Drake was a prisoner of the Styx. Eddie tells Drake, who is still conscious, only unable to move, that his manipulations have been indirectly responsible for most of the plotlines in the series, and that he had misjudged how events would play out. He tells Drake that he wants Drake and his friends to win so he can take control of the Styx. He then knocks Drake unconscious and leaves. The Second Officer, Chester, and Mrs. Burrows unsuccessfully try to open the door until Mrs. Burrows tells Colly to wake up Drake so he can open the door. This succeeds, and they escape the North Block only moments before it explodes. The Second Officer leaves the group, and Mrs. Burrows, Chester, Drake, and Colly head for the surface. They head to Eddie's warehouse to find that he has flown the coop, leaving behind only an unconscious Jeff Rawls.
Part 5 : Reunion
Drake rescues Will, Bartleby and Elliott from the fallout shelter, and takes them to the rest of the group are camping with a Gypsy band. They then leave for a safe house. Meanwhile, the Rebecca Twins return to the Colony, presenting the Old Styx the Dominion Virus, their suspiscions that Will or Elliott drank the vaccine, and the New Germainian Army. The safe house is revealed to be a country estate owned by Drake's father, Parry. Mrs. Rawls, in Highfield, is not under the influence of the Styx as it initially appeared, but is only pretending to be darklit so she can spy on the Styx for Drake. Eddie appears, foiling an attempt to make her place a bomb for the Styx, and takes her away from Highfield. Drake returns from town one morning with two things: a skateboard for Chester and a book based on Dr. Burrows's journal for Will. Will is devastated when he learns that the book, The Highfield Mole, is not a serious academic work but a novel to amuse children. In the epilogue, a news report about the closure of the three hospitals to which Drake provided samples of Elliott's blood is interrupted by a bulletin about a Styx attack on the Royal Mint, and that the police (who, along with the rest of the government, are being manipulated by the Styx) believe the mastermind behind the plot is Drake.