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. She gains the attention of the powerful Uther Doul, who is a bodyguard to the mysterious, scarred leaders of Armada known as the Lovers. 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 becomes involved with 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 physical release in each other, and commiserate that they are powerless to save their home city.
Shekel, who is learning to read with Bellis's help, finds a strange book in the Armada's library. He brings it to Bellis, and she realizes that it is the book the Lovers need to raise the avanc. Knowing that she must get a message home, Bellis destroys a large part of the Appendix which shows the equations and methods to raise the avanc.
With the book destroyed, the Lovers seek the book's writer, Krüach Aum, 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 on the island, away from Armada, to get a message home warning of the impending grindylow invasion. Armada then successfully raises the avanc and captures it – no 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, 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. Terribly damaged, Armada finally nears the Scar, and faces the unsettling horrors that accompany the breakdown of possibility. They pick up a shipwrecked friend from a different train of possibilities, chances and choices, who warns them of The Scar and that he saw the city fall into the wound of the world and everybody was killed. Mutiny follows and the people of Armada finally force the city to turn around and head back to the Swollen Ocean, the life of quiet and piracy, that they all want.
The last chapter of the book is another excerpt of Bellis's letter home, in which she realizes how much she was being used by Doul. The reader is left to question how much Uther Doul actually was in control of the events in the book, which events were simply chance and which were 'planned' possibility.
Explanation:
