Inspector Tyador Borlú arrives at the scene of a murder. A constable named Lizybet Corwi is already there, looking at the body of the dead woman. The pathologist, Stepen Shukman, determines that the woman died from puncture wounds to her chest, although there are also significant gashes across her face. Another detective, Bardo Naustin, says the dead woman was probably a sex worker. However, after Borlú and Corwi go around the area asking local sex workers if they knew the woman, none of them does. Borlú goes to Shukman’s lab, where Shukman informs him that there are no signs of sexual intercourse or self-defense, and that it seems as if the killer approached the woman from behind.
On Borlú’s request, posters go up around the city of Besźel asking for information about the dead woman. He gets a call from a colleague, Yaszek, informing him that the policzai (the police) have found the van that was used to transport the dead woman’s body. The van is owned by Mikyael Khurusch, a man with a criminal record for theft and soliciting prostitution. Borlú and Corwi interrogate Khurusch, who claims his van went missing. They learn that he has an alibi for the night of the murder.
On the Monday after the body is found, Borlú receives a personal call from a man speaking strangely archaic, accented Besź. Nervously, the man says the dead woman is named Marya, and if she is dead, he and his friends are also in danger. He says that she lived in the other city, Ul Qoma. Ul Qoma and Besźel exist in the same physical, geographic space, but they operate completely separately from one another. The man tells Borlú that he knew Marya from the underground political scene. Despite the fact that the man is calling from Ul Qoma, he admits that he saw Borlú’s poster, then immediately hangs up. Simply knowing this information makes Borlú guilty of breach, the crime of engaging with the opposite city from the one you are currently in. In Besźel and Ul Qoma, breach is “far worse than illegal.”
Without wanting to implicate Corwi in this breach, Borlú suggests to her that they look into the local unificationists—dissidents who believe that the two cities should merge into one. Borlú explains that no one knows whether the two cities began as one that divided, or whether they were founded separately. Corwi and Borlú go to a unificationist headquarters, where they meet a man called Pall Drodin. Drodin says he knew the dead woman by the (obviously fake) name of Byela Mar. He says that she used to come to the headquarters to use the library, and that she was obsessed with Orciny, the mythical third city that exists between the other two.
After receiving information faxed over from Ul Qoma, Borlú and Corwi learn that the dead woman’s real name was Mahalia Geary, and that she was a 24-year-old American PhD student in the archeology department of Prince of Wales University, a Canadian University with a campus in Ul Qoma. Borlú presents this information to the Oversight Committee, a governing body containing a mix of Besź and Ul Qoman politicians that meets in Copula Hall. Years ago, at a conference about recently discovered ancient artifacts found at an Ul Qoman dig called Bol Ye’an, Mahalia caused outrage by giving a presentation on Orciny. Borlú argues that—considering Mahalia lived in Ul Qoma and her body was discovered in Besźel—her murder must have involved breach and should be turned over to Breach, the authority charged with policing breaches. However, one member of the committee argues that Breach is an “alien power” that should only be invoked in rare circumstances. The committee reluctantly agrees to turn the case over to Breach nonetheless.
Mahalia’s parents, Mr. and Mrs. Geary, arrive in Besźel to view their daughter’s body. Mr. Geary becomes frustrated when Borlú reminds him of the restrictions involved in traveling to Ul Qoma and tells him that he will not be able to know the outcome of Breach’s investigation into the case, because they work in an extremely opaque manner. After the Gearys leave, Borlú suggests to Corwi that they keep working on the case while they wait for Breach to take over.
Borlú calls Mahalia’s PhD supervisor, Professor Nancy, who scoffs at the idea that Mahalia would be studying Orciny within an archeology department. Nancy assures him that Mahalia left her interest in Orciny behind, and that her thesis focuses on the artifacts found at Bol Ye’an, which are highly technologically advanced for their era and are rumored to have mysterious, even magical properties. Nancy says that before Mahalia lost interest in Orciny, she was interested in the work of David Bowden, an adjunct professor at Prince of Wales who wrote a book called Between the City and the City, which argues for the existence of Orciny. Borlú looks up the book online and encounters conspiracy theory websites about the existence of Orciny. He learns that Mr. Geary breached, and that he and Mrs. Geary are immediately being deported.
Mr. Geary had been carrying a piece of paper with the address of the headquarters of the True Citizens, a Besź nationalist organization. Borlú and Corwi go there, but soon after they begin questioning the people, someone calls the True Citizens’ lawyer, Harkad Gosz, who forces them to leave. The next morning, Commissar Gadlem tells Borlú that the Oversight Committee has, surprisingly, decided not to forward the case to Breach after all. Borlú is therefore still working on it, and will soon be sent over to continue the investigation in Ul Qoma.
Borlú is driven to Copula Hall, where he passes the official border and enters Ul Qoma. An Ul Qoman detective named Qussim Dhatt is waiting to greet him. As they drive away together, Dhatt warns Borlú that his role in Ul Qoma is as a “consultant” and “guest.” When Borlú asks if he can explore the city on his own, Dhatt replies that it would be best if he didn’t. The militsya (the Ul Qoman police) get a call saying that Mahalia’s best friend, another PhD student named Yolanda Rodriguez, is missing. That night, Borlú walks to Bol Ye’an and is intercepted by two members of the militsya, who politely escort him back to his hotel.
The next morning, Borlú and Dhatt go to Bol Ye’an together. They speak to Professor Nancy, David Bowden, and several of Mahalia’s fellow students. One of the security guards, a young man named Aikam Tsueh, expresses deep concern about the case. After Borlú tells Dhatt about the anonymous phone call, which he believes came from a unificationist, they go to a unificationist headquarters and interrogate the people there, but this leads nowhere conclusive. Afterward, Borlú and Dhatt go to Bowden’s apartment, where Bowden dismisses his own book, Between the City and the City, as the work of a “stoned young man.” However, he also emphasizes that most of the research in the book is still cited and considered legitimate.
The same man who originally called with the anonymous tip calls Borlú again, introducing himself as Jaris, one of the people at the unificationist headquarters. He thanks Borlú for not turning him in and explains that Mahalia believed she was helping Orciny, and told him shortly before her death that “everyone who knows the truth about Orciny is in danger.” Borlú gets a call from Dhatt saying that someone has sent a bomb to Bol Ye’an.
Showing up at the dig, Borlú learns that the bomb was addressed to Bowden and is the kind designed to target just one specific person. There is a message on it in Illitan (the language of Ul Qoma), a line from a patriotic Ul Qoman song. Borlú tells Dhatt about the phone call from Jaris, and Dhatt insists that they put aside their differences and commit to working together. This is made difficult when Dhatt’s colleagues from the militsya harass Borlú for being Besź. The next day, Borlú tracks down Yolanda, who is hiding in a derelict apartment on the outskirts of the city. Her boyfriend, Aikam, goes to visit her, indirectly leading Borlú to her. Yolanda explains that before Mahalia’s death, Orciny had been contacting Mahalia, and now Yolanda is terrified that Orciny is going to kill her as well. Borlú suggests she commit breach to protect herself, but Yolanda thinks that Orciny and Breach might be the same thing. Borlú promises that he will get Yolanda to safety via Besźel.
Bowden is missing, but Borlú manages to get in contact with him via phone. Along with Dhatt and Corwi, he makes a plan to secretly smuggle both Bowden and Yolanda into Besźel by pretending that they are militsya. However, just as they are about to pass through Copula Hall, Yolanda and Dhatt are shot. Dhatt is just injured, but Yolanda dies.
Borlú runs after the shooter and shoots him, thereby committing breach (because the shooter is in Besźel). Breach surround Borlú, and he is enveloped in darkness.
Borlú wakes up inside a kind of prison cell, which he is told is in “the Breach.” There are three people in there (Breach avatars) who do not introduce themselves by name, only as Breach. They tell him that he committed a particularly violent breach, and that it is up to them how long he stays there. They need to figure out the details of the case in order to make a decision.
Borlú walks through the cities along with another Breach avatar, who goes by Ashil. None of the citizens can properly see them. Ashil explains that they are not in one city or the other, but both. They go to the Ul Qoma University library, where they find Mahalia’s copy of Between the City and the City. They then go back to Bol Ye’an, where they figure out that Mahalia was smuggling some of the artifacts to (what she thought was) Orciny. Borlú then realizes that Mahalia wasn’t killed because she believed in Orciny, but rather because she eventually stopped believing in it, which jeopardized the smuggling operation.
Back at the Breach headquarters, Borlú realizes that a corporation called Sear and Core was behind the operation to smuggle the artifacts; they were using Mahalia in order to get the artifacts out of Bol Ye’an in order to sell them in Besźel for a profit. Orciny, it becomes clear, does not actually exist. Just as Ashil agrees to use the forces of Breach to apprehend Sear and Core, he gets news that unificationists have engineered a crash between two busloads of refugees. It is a massive breach event, and the wholes of both cities are being placed on lockdown.
Borlú and Ashil go to the Sear and Core building, where they find a representative from the company, Ian Croft, alongside a Besź social democrat politician named Mikhel Buric and two Besź nationalists. Buric admits to arranging the whole smuggling scheme for Sear and Core, boasting that he was enriching Besźel at Ul Qoma’s expense. A shootout takes place; Buric is killed and Ashil injured. Croft escapes, thereby evading punishment for his role in the scheme. After making sure Ashil is taken care of, Borlú tracks down Bowden with the help of Corwi and Dhatt, although his ability to communicate with them is limited by the fact that he is in Breach. In the confrontation that ensues, Borlú accuses Bowden of using and then killing Mahalia out of his own egoism. Bowden was the one who decided to use her as part of the Sear and Core smuggling operation, and he chose Mahalia because he wanted her to believe in Orciny in order to legitimize his scholarly work; he was furious when she realized the truth. Up until this point, Bowden has been moving in a perfectly neutral manner, such that no one can tell whether he is in Besźel or Ul Qoma. However, Borlú forces Bowden to breach, and they are both taken by Breach.
At the end of the novel, Borlú remains in Breach, unsure of how long he will be there or if he will ever get out. He now lives “in both the city and the city.”
