The Scar opens with the journey of a small ship which has set out from New Crobuzon. It is heading to the city's new colony, Nova Esperium, which lies across the Swollen Ocean of Bas-Lag. On board the ship are:
- Bellis Coldwine, a cold, reserved linguist who is fleeing for her life for her alleged connection to the events in Perdido Street Station.
- Johannes Tearfly, a scientist whose interests lie in megafauna and underwater sealife.
- Tanner Sack, a Remade criminal (that is, he has had his body surgically and magically altered as punishment for his crime) who is bound for slavery.
- Shekel, a young cabin boy who befriends Tanner.
Before the ship reaches Nova Esperium, it is captured by pirates, and the passengers, crew and prisoners are all press-ganged into being citizens of Armada, a floating city made of thousands of ships. Tanner uses his newfound freedom to embrace his remaking. He has his body further remade and the earlier, rough work perfected, becoming an amphibious sea-creature. Treated now as an equal citizen rather than a prisoner or slave, Tanner's loyalties fiercely lie in Armada.
Bellis meanwhile despises her new life as a librarian for the city's vast collection of stolen books, and yearns for home (somewhat ironically, as she was originally fleeing it). She gains the attention of the powerful Uther Doul, bodyguard to the Lovers, the mysterious, scarred leaders of Armada. Doul, for his own reasons, involves Bellis much more closely in the city's matters. She soon becomes privy to a plan formulated by the Lovers to raise a mythical sea creature known as the avanc. Simultaneously, she meets a New Crobuzonian spy named Silas Fennec, who reveals that the grindylow of the Cold Claw Sea are planning war on New Crobuzon. Silas was on his way home to warn his leaders of this war (thus saving the millions of innocents who might be slaughtered by the grindylow) when he was captured by Armada. Bellis and Silas find romantic interest in each other, and commiserate that they are powerless to save their home city.
Soon enough Bellis, in Armada's library, stumbles across the information that the Lovers need to raise the avanc. Knowing that she must get a message home, Bellis destroys that information. This forces the Lovers to seek Krüach Aum, now the only person who knows how to summon the mythical creature. Armada mounts an expedition to his unnamed island home, which is the island of the dreaded Anophelii (a horrific and deadly race of mosquito-people). The Lovers find Aum and the information they need, while Bellis uses their time out of Armada to get a message home, to warn of the impending grindylow invasion. Armada then successfully raises the avanc and captures it – a mean feat, as the avanc is an immense creature, several miles long. The Lovers' true plan is finally revealed: to use the great speed and pulling power of the avanc to find the fabled Scar, a place in the world where reality breaks down and anything is possible. The Lovers see this as a source of ultimate power.
On the journey far into unmapped waters, numerous matters threaten the city. Silas Fennec's actions, which have been far from honest all along, single-handedly bring down the fury of the New Crobuzon navy and the inhuman wrath of the grindylows. Following this a civil war breaks out within the city. Then, terribly wounded, Armada finally nears the Scar, and faces the unsettling horrors that accompany the breakdown of possibility.
- Bellis Coldwine
- Tanner Sack
- Uther Doul
- Silas Fennec
- The Lovers
- The Brucolac
- Johannes Tearfly
- Krüach Aum
- 2002 - Philip K. Dick Award
- 2003 - Arthur C. Clarke Award
- 2003 - Hugo Award for Best Novel
- 2003 - British Fantasy Award for Best Novel
- French - Les Scarifiés
- German - Leviathan and Die Narbe