The novel is divided into two different stories, one story taking place in the past, in the 18th century and the other in the present. The chapters are mixed but the first chapter is set in the 18th century and focuses on a man named Nicholas Dryer.
The book begins with the note "To Giles Gordon’’ and then with a short introductory paragraph presenting a little bit of information regarding the background of the story. The author begins by writing how in 1711 an act was passed that allowed seven new Parish Churches to be built. The architect’s name was Nicholas Dryer and he chose to work alone, helped only by his assistant.
The first part of the book begins with a conversion between the architect, Dryer, and his assistant, named Walter. Dryer gives instructions to Walter on how to draw what he wants him to do dryer goes outside for a walk and when he returns he is displeased to see his assistant sitting instead of working as he should have. The two talk about the Churches until Sir Christopher walks in and tells Dyer that he needs to have the plans for the Churches ready as the commission is there and wants to see them and find more about the progress of their work. Dryer dictated a letter to the board after which he left into the night.
Dryer hailed a coach and then went to the other part of the town where he stopped in front of a door and knocked on it.
Dryer takes a moment here to present his past. He was born in 1654 into a poor family and his father was sure that both the newborn child and the mother would die. Nicholas did not die and his mother also made a fast recovery. Dryer attended a charity school but he mentions how he was different from other boys in the sense he was not interested in the things normal boys were interested in.
Dryer had a passion for reading and he would borrow books from whoever was ready to lend them to him. Dryer chose to stay separated from the rest of the kids most of the time and he liked to walk on his own through London and through the poorest places in the city.
Dryer then mentions something that had happened when he was 11 years old and that is the plague which affected the city. Dryer’s mother was affected as well and while the city officials urged the family to remove her from the house, the father refused and insisted that she remains there were he can take care of her. The father urged Nicholas to flee and he did it before the house was marked and closed as being unclean. The father became soon affected as well but Nicholas did not help any of them and just sat and watched them die. After that, Nicholas escaped from the house when people came after the dead and he just sat and watched as his parents were wheeled away.
Nicholas followed the cat until it reached a pit where the bodies were all thrown into. Nicholas wandered on his own all night, unsure of what to do and where to go.
He then stops talking about his past and returns to the present, in his office together with his assistant. They have a brief discussion and then he thinks back to his past when he was a young boy living in the streets.
He is spotted by a man with two other women and the man approached him and called him over despite being told by the women not to. Nicholas ponders whether he should follow the man and the woman and he decides to do it when he is sure they are not infected by the plague and when he is sure they are not evil spirits. Nicholas does not tell them his real name but rather claims his name is Faustus.
Nicholas is taken to a building where other women and men are and he is given a strange drink to consume. He was then given a pair of glasses and through those glasses he was able to see his mother, the way she locked before she died. After that, Nicholas was left alone in the room and felt asleep.
Nicholas remained with the group and was introduced to satanic teachings while there and he grew to accept them. Everything he was thought until then was untrue and he learned new things about the real God of the world, Satan, and learned how he should worship him.
Nicholas is put to drink a strange concoction and he falls into frenzy, a time during which he sees his mother just as she was before she died. Nicholas even envisioned her in her room, working with her needles. The strange man tells Nicholas that seven churches must be built for Satan and the narrator returns to the present time when Nicholas stays by his table.
Nicholas then recalls another story, about a boy of about ten years old named Thomas. The boy was the son of a mason whom was present when the church was built. The boy climbed up one of the church towers but he slept and felt to his death. In that moment, Nicholas has a revelation: for his buildings to succeed, there needs to be given a blood sacrifice.
The second chapter takes place in the present, at the site where Nicholas Dryer’s parents died. A boy named Thomas Hill lives in the area with his mother but neither like it. The mother dislikes the Church her son visits often and Thomas has troubles making friends and is often bullied at school.
As a way of escaping, Thomas reads everything he can find but he manifests a particular interest for stories in which forces of evil appear.
One night, Thomas sees a strange man from his window. A few days later, Thomas goes near the church and there he sees a couple fondling each other. Scared, he runs towards the church and into one of the tunnels to hide from them. After this incident, Thomas begins to touch himself and to explore his sexuality. He also notices how he is followed by a man looking like the one he saw from his window a couple of nights before and so Thomas decides to follow him. Thomas is discovered and he runs towards the church where he hides in one of the tunnels again.
Unfortunately, Thomas injures his leg in the tunnel but he still tries to escape by finding a way out. It is implied that maybe Thomas passed out in the tunnel and when he woke up, he saw the face of his dead father and another group of strange men and women. While Thomas’s mother looks for him desperately, Thomas remains in the tunnel with the strange group. He also hears a strange voice, urging him to go on, almost as if he was climbing something.
The third chapter returns to Nicholas who is sick in bed. He continues to be involved in the building of the churches even though he is incapacitated and gives instructions to his assistant. Nicholas tries to include in the architecture of the church various elements to symbolize his devotion for the occult.
Nicholas also talks more about his past and the time he spent with Mirabilis. Nicolas continued to be thought by him but he stayed on the streets during the night. When he was 14, he was taken in by one of his aunts and Mirabilis disappeared forever.
At the young age of 14, Nicholas began working with a mason named Creed and his interest in architecture grew. He was a talented young man and he was quickly noticed by other people as well. Thus, in only two years, he started working under Sir Christopher who helped him grow and cultivate his talent.
After Nicholas talks about his past, he mentions the second man he saw die, a beggar named Ned. While in the case of Thomas, the son of the mason, he was not directly involved in his death, this time he urged the man to kill himself, even guiding the knife so that the man would kill himself faster.
The fourth chapter takes place in the present time, and the narrator focuses on three beggars, living in an abandoned house. One of the people in the house is named Ned, a man who was once a printer. He became homeless after he told an untrue story to his friends and became afraid his colleagues will tell his boss about it. Ned left is home and started living on the streets. He started begging to survive and eventually ends up in London were he meets a strange man dressed in black. Ned meets with the man again a few times and the man tries to convince Ned to kill himself. The chapter ends with Ned going to the Limehouse church where he dies.
In the fifth chapter Nicholas Dryer is criticized by his peers for his work-ethics and for the way he chose to deal with various problems. Also, the practices and the way Dryer behaved in secret were exposed to some so he partners with another man named Joseph. The deal between the two is that Nicholas will continue building and Joseph will be the one killing and presenting the sacrifices.
The third church being build is at Wapping and Dryer is unhappy with how some people criticize him and talks behind his back. He decides to fire them and bring in new people who would be more obedient. Around the same time, Nicholas also receives a letter threatening him and he becomes scared someone will find about his actions and turn him in to the police.
The chapter ends with the third sacrifice, a boy killed by Joseph and then buried in the foundation of the church.
The sixth chapter presents a new character, an inspector named Hawksmoor who looks into the strange death of three people. He goes to see the body of Thomas and reads the reports on the other murders. All three people died by being strangled but no prints and other clues were left behind. The end of the chapter also reveals the name of the third victim, Dan Dee.
The seventh chapter focuses on Dryer once more and describes his behavior. A strange man comes looking for him and Dryer is sure the man is Hayes. Thus, Dryer invites Hayes to go drinking with him and when he becomes extremely drunk he takes him to a secluded place and kills him. After that, he seeks the services of a prostitute.
The eight chapter describes the discovery of the death of a young boy named Matthew Hayes in a church called St. Mary. Near the church, another skeleton, an old one was discovered during the excavation of the place but no one thinks anything of it. He also disregards information about a strange man following the boy and does not consider it as being important for the solving of the mystery.
A man named Brian Wilson confessed to the murder of Matthew Hayes but Hawksmoor refused to believe him and set him free. This made Walter suspicious and also worried because his superior behaved in an unnatural manner and so he decided to follow him.
Hawksmoor receives another letter from a person who does not reveal their identity and who claims he is the author of the killings.
In the ninth chapter, Dryer tries to remove the incriminating evidence that could lead up to him. Hayes’s body is discovered by Walter and Dryer is informed by it. Dryer helps to organize Hayes’s funeral and after that he goes out to drink.
Dryer changes his approach and dresses as a beggar to try and attract people he can kill. Around that time, Walter becomes ill and during one of his visits, Dryer finds that Walter was the one who wrote the letter that scared him.
Dryer is also replaced by a man named Mr. Vanbrugghe but he decides to continue with his sacrifices and sets a date when he planned to make the next sacrifice.
The tenth chapter describes the discovery of a new victim, with the same marks as the ones before. He discovers a book with clues and also a potential witness but he is discharged from the case because of the way he was influenced by it.
Chapter eleven is the last chapter focusing on Dryer. The actions take place after Walter died and Dryer is focused on building his last church. His condition deteriorated as well and he started seeing strange people and hearing voices. The chapter ends with him going into the church and finding peace there.
The last chapter shows how Hawksmoor was affected by the events that took place in his life and how he was destabilized by them. The book ends with Hawksmoor going to the last church built by Dryer.