In a post-apocalyptic world where mobile Traction Cities are in conflict with the Anti-Traction League, a reanimated corpse called Stalker Shrike is brought back to life for the second time by Doctor Oenone Zero, a member of the extremist Anti-Traction group Green Storm. Shrike has lost all his memories of the past and of Hester Natsworthy, who was like a daughter to him. Doctor Zero tells him that he will serve the Green Storm now because she has rebuilt him to be a bodyguard for Stalker Fang, Green Storm’s leader.
Sixteen years after the Traction City of Anchorage landed on an island in America, it is now well established as Anchorage-in-Vineland, a static settlement. Wren Natsworthy, teen daughter of Tom and Hester Natsworthy, longs for adventure. She gets her wish when Gargle, the leader of a group of thieves called the Lost Boys, comes to Vineland to meet his old friend Caul, Anchorage’s eccentric engineer. Caul refuses to help Gargle steal a book, so when Gargle discovers Wren spying on him, he asks for her cooperation. Wren agrees to look in the library for the volume Gargle wants, known as the Tin Book.
Wren asks Freya Rasmussen, the former Margravine of Anchorage, about the Tin Book. Freya shows Wren the book. Then Wren goes to ask Gargle why it’s so important. Gargle says that Professor Pennyroyal (who stole the Natsworthys’ airship the Jenny Haniver, shot Tom in the chest and stranded them both on Anchorage 16 years ago) has made life hard for the Lost Boys.
The Lost Boys used to burgle Traction Cities by secretly attaching their limpet ships to the bottom of cities, but when Pennyroyal wrote a best-selling book describing the limpet ships, they could no longer burgle the way they used to. Gargle says the Tin Book contains plans for giant submarines, and he wants to turn the Lost Boys’ underwater city of Grimsby into a mobile city so they can safely search for places to burgle.
Wren agrees to steal the book for him, on the condition that he takes her with him to Grimsby when he leaves. When Wren leaves her house to run away with Gargle in his ship, the Autolycus, Caul warns the Natsworthys, and Hester goes to find Wren. Hester shoots and kills Gargle, but is too late to save Wren, who is kidnapped by the 10-year-old Lost Boy Fishcake and taken away in the Autolycus.
Wren and Fishcake encounter a message from the raft resort city of Brighton, saying that the families of all the stolen Lost Boys are looking for them. If they come to Brighton, they can be reunited. Fishcake is excited about the chance to find his family, and Wren encourages him to steer the Autolycus to Brighton so she’ll have a chance of escaping him.
In Brighton, Wren and Fishcake discover that the message is a trap. They are taken as slaves. Pennyroyal is now the mayor of Brighton, and he allows slave traders to operate freely in his town.
Fishcake reveals Grimsby’s location, and Brighton drops underwater bombs on Grimsby, destroying it. Through quick thinking, Wren is able to disguise her true identity and ingratiate herself with Pennyroyal by flattering him and saying she’s a big fan of his books. Meanwhile, the slave trader Nabisco Shkin convinces Fishcake to tell him where Anchorage-in-Vineland is, because Shkin plans to enslave everyone living there.
In Tienjing, the capital city of the Anti-Traction League and Stalker Fangs’ headquarters, Doctor Zero wants to kill Stalker Fang, but can’t work up the courage to do so. Shrike wants to protect Stalker Fang, but he finds that he can’t foil Doctor Zero’s plans because she has made him incapable of harming her in any way.
Freya, Caul, Tom and Hester all set out in Caul’s limpet ship, the Screw Worm, to find Wren. They discover the wreckage of Grimsby, but find the Town Hall still intact enough that they can dock the Screw Worm and go inside. They find several very young Lost Boys and Girls, and they meet Uncle, who is old and nearly blind. Caul suddenly takes Hester’s gun and points it at his friends, joining Uncle’s side and locking them into jail cells, but Caul frees his friends when Uncle falls asleep.
Uncle wakes up and threatens everyone with a gun, but then he accidentally kills himself by shooting down a balloon holding monitor screens, which fall and crush him. Caul and Freya decide to take the limpet Naglfar and carry the Lost Boys and Girls back to Vineland for safety, while Tom and Hester take the Screw Worm to Brighton to search for Wren. A few months after Naglfar lands in Vineland, Caul and Freya are married.
In Brighton, Wren becomes a house slave for Pennyroyal and his wife, Boo-Boo. They live in the mayor’s floating residence of Cloud 9, which is tethered above the city of Brighton with cables. Wren unsuccessfully tries to befriend fellow slave Theo, who was once a member of the Green Storm.
Brighton drops anchor near Africa so Traction Cities can send their people to Brighton to celebrate the Moon Festival, the biggest holiday across all societies. The night before the festival starts, Wren tries to steal Pennyroyal’s ship, the Peewit, but is delayed when a man is murdered in Pennyroyal’s quarters. The man was trying to steal the Tin Book, which Pennyroyal took from Wren when she came to Brighton.
Tom and Hester attach the Screw Worm to Brighton on the day of the Moon Festival and come aboard to search for Wren. Tom is captured by Shkin and taken to his slave-holding headquarters, the Pepperpot. Shkin finds Wren and blackmails her into stealing the Tin Book for him in exchange for her father’s life. With Theo’s help, Wren takes the Tin Book from Pennyroyal’s safe, but then they both discover that someone has cut the lines binding Cloud 9 to Brighton.
Hester breaks into the Pepperpot, killing guards along the way. She frees some captive Lost Boys, who cause a huge commotion, enabling her to rescue Tom. While at the Pepperpot, Tom has been treated kindly by Fishcake, and he wants to take Fishcake back to Vineland. Reluctantly, Hester agrees.
Doctor Zero flies aboard Stalker Fang’s flagship, the Requiem Vortex, on a mission to attack Brighton and steal the Tin Book. The Requiem Vortex bombs Brighton with kamikaze ships called Tumblers, and the Green Storm board Cloud 9, capturing Wren and Theo.
Stalker Fang takes the Tin Book but is suddenly attacked by Shrike, who is under the control of Doctor Zero. Before Shrike pulls Stalker Fang to pieces and throws her to the ground below Cloud 9, she tells Shrike that the Tin Book contains codes to control ODIN, a satellite weapon that could easily destroy any city. Shrike runs away and hides on Cloud 9.
Doctor Zero expects that Stalker Fang’s second-in-command, General Naga, will execute her for disposing of Fang, but instead he commends her. General Naga takes all of Cloud 9’s remaining inhabitants aboard the Requiem Vortex and flies back to Tienjing. Wren and Theo hide and remain on Cloud 9.
In the chaos of the Green Storm’s attack on Brighton, Tom and Hester lead Fishcake to the Jenny Haniver, which they find docked in a museum. Hester flies away without Fishcake, which horrifies Tom. Fishcake escapes Brighton and swims to the African shore where he finds the remnants of Stalker Fang, who commands him to put her back together so she can unleash ODIN’s power.
On Cloud 9, Wren discovers a wounded Pennyroyal, who tells her that his famous novels are all lies except for the part about her mother betraying Anchorage because she was jealous over Tom. The Jenny Haniver lands on Cloud 9, where Tom and Hester are reunited with Wren, who introduces them to Theo. As soon as Hester sees Pennyroyal, she knocks him to the ground and attempts to kill him so he won’t tell Tom she once betrayed Anchorage.
When Wren defends Pennyroyal and reveals that she also knows Hester’s secret, Hester threatens Wren with a knife. Wren tells Tom what Hester did, and Hester decides to stay behind on Cloud 9, which is crashing to the ground, because she can no longer live happily in Vineland now that Tom knows her true nature.
Tom, Wren and Theo escape in the Jenny Haniver. Meanwhile Shrike, who has regained his memories of loving and raising Hester, discovers her as Cloud 9 crashes, then carries her unconscious body away from the wreckage and into the desert.