Part 1: Breaking Cover
The story opens with Sarah Jerome, Will's biological mother, dismounting from a bus and going on foot to a concealed chamber built into a bridge in a remote rural location. There she collects a letter that states her brother Tam is dead because Will betrayed him to the Styx. Sarah is filled with grief, and struggles to believe that her son is capable of this.
Meanwhile, Will and Chester are overjoyed to be reunited once again as the Miners' Train travels down through the Earth on its way to the Deeps. Will's younger brother, Cal, is also with them. The train passes through a series of storm gates and, on the final approach to the Miners' Station, the three boys jump from it. Having escaped detection at the station, they travel further into the Deeps, where they are attacked by carnivorous bats and are forced to take shelter in an old, deserted house. Inside the house they find evidence that Will's stepfather, Dr Burrows, has already been there.
Sarah adopts a disguise, allowing her to become a woman who has the authority to interview a deranged Mrs. Burrows, who currently is residing at Humphrey House. However, when her fear that Will actually killed Tam clouds her judgment, Mrs. Burrows quickly realizes the fake, forcing Sarah to flee. Soon, she is acquainted with a much skinnier, much weaker Bartleby, who takes her to a hiding place. There, a few days later, Rebecca and the Styx show up and make her believe for sure that Will killed Tam. Rebecca tells her that she knows where Will is, and that he is forcing Cal to come with him, and, if she didn't act soon, Will might kill him also. Also: Bartleby was Cal's Hunter in the Colony, and now he is hers. Finally, they explain that Cal and Bartleby shared a strong bond, and, because of his love for Cal, Bartelby would be able to track him down anywhere...
Finally, Dr. Burrows is shown as still alive. He has been accepted by a strange, gentle group of people called Coprolites, who live in the Deeps. Sadly for them, a special detachment of the Styx called Limiters has been killing them. Having been left provisions by the Coprolites before they moved camp to a safer location, Dr. Burrows packs up and leaves, continuing further into the Deeps, keeping his notebook with him at all times.
Part 2: The Homecoming
Sarah is taken to see her mother, Grandma Macaulay, in her old home. Grandma Macaulay has been persuaded by the Styx that Will was responsible for Tam's demise, and she is full of vengeance and asks Sarah to exact revenge on the boy. Sarah is then escorted to the Styx Garrison where she rests, is given military training, and is also subjected to sermons from The Book of Catastrophes.
Concerned that their food supplies are running low, Will and Chester follow Cal down into an opening of the floor of the Great Plain (a massive cavern with a plain stretching for miles), where Cal enters a cavern filled with unidentified pipe-like organisms. As he stumbles, Cal touches one of these organisms, then collapses. Will and Chester discover that the boy isn't breathing, but they are forced to flee the cavern in order to save their own lives.
Topsoil, it is dawn in England, and Rebecca and a squad of Styx are on the rooftop of Admiralty Arch, overlooking Trafalgar Square, with baskets of doves. Attached to the leg of each bird is a small metal ball which, when melted by the sun, will release a small amount of a non-deadly form of the virus that the Styx have been working on. The section ends with Rebecca cheering the doves on to "Fly, fly, fly!".
Part 3: Drake and Elliott
After his brother's death, Will is beside himself with grief, and Chester becomes increasingly concerned about the strange way he is acting. Shortly thereafter, they witness the execution of a group of Coprolites by a patrol of Styx Limiters. Will's abnormal behavior takes over again, and he asks for a piece of chewing gum. Before he unwraps it, knives are put at both boys' throats. A man speaks, telling them to bury the gum, and then to come with them. With no alternative but to do what they are told, Will and Chester comply.
The two strangers introduce themselves as renegades, namely Drake and Elliott. Drake soon realizes it is important to keep Will alive because he thinks Will may be the cause of the increased Styx presence in the Deeps, and also because he discovers Will is Sarah Jerome's son. For the most part, Elliott maintains a hostile attitude towards the boys, except for Chester. Cal, who Will and Chester feared had perished in a "sugar trap", is resuscitated by Drake.
Sarah persuades Joseph, her Colonist friend, to allow her to leave the Styx Garrison so she can revisit the Rookeries, a place where the most deprived Colonists are left to rot, and where she and her brother Tam played as children. However, as she passes through the area, she is recognised and hailed as a hero. As she emerges from the Rookeries, she is met by Rebecca who tells her they are to leave for the Deeps on the Miners' Train.
Topsoil, the virus created by the Styx scientists has been spread, and is wreaking havoc on England. The symptoms are some coughing, and swollen eyes, which make reading and looking at objects very hard. A grouchy Mrs. Burrows is visited by a man who has a distinguished voice and likes boiled eggs, hence Mrs. Burrows's nickname for him: "boiled-egg man". Boiled-egg Man tells her everything will be fine, when, in fact, it is steadily getting worse. Soon, a woman named Mrs. L dies, and not long after that, the laboratory that researches the virus is burned, and, when Boiled-egg Man appears on the news, claiming that there was no case of arson and that it was an experiment that blew the lab up, killing five scientists, Mrs. Burrows, who believes the opposite, becomes very angry.
Part 4: The Island
When they are attacked by Limiters, Will becomes separated from Drake, Elliott, Cal and Chester, and without any food or light, becomes completely lost in the lava tubes for several days. He eventually emerges from the lava tubes, and is reunited with Chester. Meanwhile, Drake and Elliott take Cal with them as they search the Great Plain for Will, and here they come to a place called the Bunker, which it appears was once used to breed Coprolites. One area in the Bunker is now being used to test the Dominion virus, which the Styx intend to use to decimate a large proportion of the Topsoil population. After a Styx ambush, Drake is captured outside the Bunker, while Elliott and Cal manage to escape. The two return to Will and Chester, and then Elliott leads them all to an island in a subterranean sea.
Elliott takes Will to scout, and they discover that Drake is being tortured. Elliott decides to kill him to put him out of his misery. When they return to the camp, Elliott captures a "night crab" for a meal, which Will excitedly identifies as a relic species of Anomalocaris. However, the Limiters, along with Sarah, find the camp on the island. Elliott takes the group on the run, escaping in a boat they built. To kill the Limiters on the island, Elliott blows it up using an explosive cache.
Part 5: The Pore
Dr. Burrows comes across a temple-like structure, built by a civilization that worships a sun. He discovers a hoard of large dust mites and then comes across a huge, mile-long hole, which he accidentally falls into.
Elliott's initial plan is to take the boys to a place called the Wetlands, where they will allegedly be safe. She takes them through a tunnel, but before long, Bartleby appears, and Cal is delighted. Elliott shoots an advancing stranger, which turns out to be Sarah Jerome. Will assures her that he did not kill Tam, then he and the others continue on their way. At her insistence, because she is too badly injured and would only slow them down, Sarah stays behind. They escape through a rock formation called the Sharps, but a Limiter appears. The boys deal with him, with a shaken Cal killing him. Elliott blows up the Sharps, letting the group safely escape.
They eventually come across the huge hole; the same one Dr. Burrows fell into. It is identified as the Pore, which stretches even deeper into the Earth's surface. Before long, they are ambushed by Rebecca, and she reveals that there is not one but two of her; they are twins, and they have been alternatively living in Will's home, posing as his younger sister. They reveal their plot to kill all Topsoilers with a deadly virus called Dominion, which was extracted from the Eternal City by the Styx Division. The twins order the Limiters to open fire; Cal is killed as a result. Will, Elliott, Chester, and Bartleby are blown into the Pore by the Styx's heavy guns. The Rebecca twins presume that they have fallen to their death, and the Limiters cease fire.
Sarah, who is close to death from her gunshot wounds, witnesses this. She draws upon her last remaining strength and, in a headlong rush at the Rebecca twins, takes them over the edge of the Pore with her.
Several days later, Drake is shown Topsoil as he observes a Colonist who is, in turn, observing Mrs. Burrows. It is clear that he wants to exact his revenge on the Styx for the deaths of Elliott and the boys. The book ends when he dials a phone and waits for an answer.
Character Arcs during Deeper Edit
- Will: He usually stayed the same throughout the developing of Deeper, only being jealous of Chester getting along with Elliott and being mostly focused on finding his father. He's caring about Cal, and they get more closer. He keeps being extremely curious about his surroundings. He's more serious and mature after shooting 'Drake', as he starts to understand the situation they are involved in.
- Cal: At the beginning of Deeper, Cal was rude towards Chester, and a bit of a nuisance. He changed after his close experience with death, and in Will's words, he became more 'stoic'. While staying with Drake, he strove to improve, trying to become a more valuable member of the group despite being just a kid.
- Chester: After finding Drake and Elliott, Chester started changing his personality, becoming more self-confident and independent. He learned quickly how to move in the Deeps, usually going on patrols with Elliott. His friendship with Will became more distant, and they even had a fight at the end of the book where he blamed Will for all their problems. He apologized after, and they became friends again. During the following books, their friendship grew stronger than ever.
- Oddly, in the US cover they removed Elliott's rifle and showed her holding a lantern instead.
- It was the longest book in the series, with 643 pages.
- It received the most positive critics of all the series, quickly followed by Freefall. However, in ratings from the general public Deeper is placed fifth with a 3.92/5, only surpassing Tunnels that has a 3.56/5 score.
- It's the first and only one to have a sneak peek at the following book in the series.