The story takes place within the city of New Crobuzon; the entire novel is set here. Isaac Dan der Grimnebulin is the novel's protagonist; a scientist who conducts experiments and independent research within his laboratory in Brock Marsh. Isaac's partner Lin is a kephri and a famous "gland artist" within the city. Later, Isaac meets a garuda named Yagharek who was exiled from his homeland after raping a fellow member of his species. The punishment for his crime led to his wings being severed during a public execution; he travels to New Crobuzon in the hope of regaining his ability to fly by acquiring new wings. Isaac makes a promise to Yagharek that he'll restore his wings and the garuda offers a decent sum of money to the scientist after he begins his research. During this time, Lin was offered the opportunity to create a sculpture of a criminal kingpin known as Motley; she dedicates her days to the artwork which remains in the attic of one of Motley's operating buildings. Motley makes a significant amount of money from trading hallucinogenic drugs; the substance is the extracted milk from several worms which he keeps in captivity. In order to complete his contract for Yagharek, Isaac enlists the help of a criminal named Lemuel who finds a variety of winged creatures who the scientist aims to study and gain knowledge on the physiology of flight.
After the experimental birds arrive at Isaac's laboratory, he finds that one of the creatures is a large worm. He decides to feed it a hallucinogenic drug known as Dreamshit which causes the worm to excessively grow and out-size its cage.Consequently, the worm flees the laboratory and manages to escape; Motley discovers this and assumes that Isaac is a potential rival drug-trader. As a result, he holds Lin ransom within his attic, threatening to kill her if Isaac refuses to return the worm. Lemuel reminds Isaac that Motley has no incentive to keep Lin alive, so returning the worm will be ultimately pointless. With the assistance from his friend Derkhan, Isaac finds out that Motley had purchased the worms from the government of New Crobuzon; the state attempts to quell the various rebellions within the city and recapture the escaped slake-moths who're incredibly dangerous to the population. The creatures are able to essentially harvest people's consciousness and kill them; this occurs on several occasions which rouses the city into action against the slake-moths.
New Crobuzon's government use the help of a spider called the "Weaver" in their goal of recapturing the moths. Unfortunately, the spider refuses to co-operate and collaborates with Isaac and his team instead. Realising the potential of one of his creations known as the "Crisis Engine", Isaac meets the Construct Council in one of the cities rubbish dumps. These near-sentient robots are able to harness the engine's power by transferring its energy into another human. After finding the location of the slake-moths nest, which lies in the home of the cactacae called the "glasshouse", they kill a single moth and destroy their eggs. The moths finally converge on Perdido Street Station and the battle unfolds between Isaac's team and the monsters. By utilising the crisis engine, they manage to kill all but one moth, who eventually returns to its original home in Motley's attic, exactly where Lin is being held. During their confrontation, the moth harvests half of Lin's consciousness, essentially lobotomising her and significantly diminishing her cognitive capacity. The group manage to elude Motley, and the final moth flies from the attic into the night sky whilst Isaac, Lin, Derkhan and Yagharek seek refuge in a building within the centre of New Crobuzon.
Yagharek informs Isaac about his crime and the reason why he was forced to leave his homeland; Isaac is disturbed by this new information and doesn't complete his contract with the garuda after learning about why he lost his wings. Eventually, the garuda who was Yagharek's rape victim reaches the house where they're staying and insists that Isaac not restore the garuda's wings. The scientist agrees which reinforces his decision, and soon decides to leave New Crobuzon with Lin and Derkhan, and they walk out into the night. Yagharek writes a note about his feelings surrounding his crime and chooses to remain in New Crobuzon and forge a new life for himself in an attempt to erase his previous mistakes. His victim returns to the Cymek desert, as she wasn't searching for retribution but simply closure regarding Yagharek's crime.
- Isaac Dan der Grimnebulin
- Derkhan Blueday
- Lemuel Pigeon
- Mr. Motley
- Mayor Bentham Rudgutter
- Montjohn Rescue
- Construct Council
- The Weaver
- Benjamin Flex
- Lucky Gazid
- Fratel Sanchem Vansetty
- Jack Half-a-Prayer
- 2002 - Nebula Award for Best Novel
- 2002 - Hugo Award for Best Novel
- 2001 - Arthur C. Clarke Award
- 2001 - British Fantasy Society's August Derleth Award
- 2001 - Amazon.com Editor's Choice Award in Fantasy
- 2002 - Premio Ignotus Award for Best Foreign Novel (for the Spanish translation)
- 2002 - Kurd Lasswitz Award for Best Foreign Novel (for the German translation)
- Germany: Die Falter and Der Weber
- Portuguese: "Estação Perdido"