They are fortunate enough to be rescued by Anchorage, once a thriving Traction city that relied primarily upon trade, but which has now been devastated by an excavated biological weapon that killed nearly all of the population. The city is now ruled by Freya Rasmussen, the young margravine who was suddenly thrust into power after her parents died from the plague. The people of the city are desperate for sanctuary and have set a course for North America, which has been a radioactive wasteland since the events of the Sixty Minute War. Freya, however, is convinced that they will find a land of lush greenery, which Pennyroyal claims to have seen on a voyage to the Dead Continent many years ago. She is delighted to find that the professor is onboard her city and treats all three of them as honoured guests. Pennyroyal, however, is less than pleased to hear that Anchorage is making for America.
Tom and Hester set about repairing the Jenny Haniver, though Tom finds that he enjoys Anchorage. Hester, on the other hand, is jealous of his growing closeness with Freya, and disturbed by the sightings of "ghosts" in the city. Eventually she sees Tom kissing Freya, and flies away from the city in the Jenny Haniver, heartbroken.
Hester intends to sell Anchorage's course to the predator city of Arkangel, with the deal that when the city eats Anchorage, Tom will be returned to her. She makes this deal with Piotr Masgard, the leader of Arkangel's "Huntsmen" - armed warriors who capture cities by airship and then order them into Arkangel's jaws. Returning to the Jenny Haniver, however, she is drugged and kidnapped by a Green Storm informant.
Tom has been lamenting the loss of Hester and regretting kissing Freya. He and Pennyroyal are now stranded on Anchorage, as the Jenny Haniver was the only airship on the city. He is also shocked when Pennyroyal miserably confesses that he is a fraud - he never actually went to America, and based his entire book off an old explorer's map in the Reykjavík library, which was stolen many years ago.
In despair, Tom makes another shocking discovery: the "ghosts" who have been sighted around the city are actually thieves, operating out of a parasite submarine attached to the bottom of the city. They call themselves Lost Boys and work out of a larger group in the secret underwater city of Grimsby. With their secret blown, they kidnap Tom and leave the city, taking him back to Grimsby.
Tom develops a sort of friendship with the boy Caul on their trip back to Grimsby. Caul tells him that the city is ruled by "Uncle", a man who founded it long ago as a base of thieves. The Lost Boys use limpet submarines to attach themselves to raft-cities and ice-cities, robbing the inhabitants. When they arrive in Grimsby Tom is taken to see Uncle, who tells him there is something valuable in Rogue's Roost, which he wants Tom to steal for him. In return Tom will have the chance to rescue Hester.
Tom agrees and Caul takes him to the Roost. He climbs a ladder up the rocky cliffs to infiltrate the base but is soon discovered. This was the Lost Boys' plan all along, it is revealed - they were merely using Tom as a decoy to mount their own infiltration. Caul, however, does not want to see Tom die, so he blows up the charges the Lost Boys had planted prematurely, risking their operation but saving Tom and Hester.
In the confusion the Lost Boys make their way to the chamber where the Stalker Fang is kept. This is apparently what Uncle wanted to steal, as she betrayed him when they were young and he now wants revenge by making her his slave. The Stalker easily kills the Lost Boys however, with only Caul and a few others escaping in a limpet. It pursues Tom and Hester into a hangar where the Jenny Haniver is kept, but before it kills them it suddenly remembers their faces. The Stalker lets them escape, and then takes command of the Green Storm forces.
In Anchorage, which is now west of Greenland, Arkangel is catching up to the city and the Huntsmen have been dispatched. They easily overpower Anchorage and leave it helpless on the ice, but with a day to go before Arkangel arrives Tom and Hester make it back to the city, finding it eerily deserted. They discover Pennyroyal is the only one who has escaped notice by the Huntsmen. Hester sends Tom to hide in safety, intending to kill the Huntsmen herself. She tells Pennyroyal to run out and make a diversion. When he refuses out of fear, she confides in him that it was her who sent Arkangel after Anchorage. Terrified by her ruthlessness, he runs out and is spotted by the Huntsmen. She uses the distraction to kill those by their airship, and then heads up to the palace where the city's populace are being kept. Tom sees Pennyroyal running off, and chases him.
Hester liberates the palace and kills the last of the Huntsmen, while Tom confronts Pennyroyal, who is attempting to fly off in the Jenny Haniver. Attempting to scare Tom off, Pennyroyal accidentally shoots Tom in the chest. He then steals the airship, and escapes.
Arkangel is still pursuing Anchorage, but accidentally heads over thin ice and is trapped. Anchorage escapes on an ice floe, but with the revelation that Pennyroyal is a fraud they have lost hope in the salvation of their city waiting in America. Caul then arrives with the Reykjavik map, and convinces them to keep going.
Pennyroyal makes it back to the safety of the Hunting Ground, and soon publishes a book retelling the events of Anchorage's flight west, casting himself as the hero. Arkangel is evacuated and eventually sinks to the bottom of the ocean as the ice thaws in summer. In Asia, the Green Storm topples the old Anti-Traction League under the leadership of the Stalker Fang, setting up events for the war that takes place in the following books.
Anchorage eventually makes it to Newfoundland, and finds it verdant and lush. Tom has survived his bullet wound, but is still very weak. Hester reflects that the city will be secret and safe in this new land, and is pleased to discover that she is pregnant.