Six months after escaping the Green Storm’s attack on the floating city of Brighton and parting ways with Wren Natsworthy, Theo Ngoni has returned to his home country of Zagwa. He hears news of the wider world. After the supposed demise of the undead cyborg Stalker Fang, General Naga leads the Anti-Tractionist extremist group Green Storm and has surprisingly called a truce with all the Traction Cities, promising an end to the war that has been wrecking the planet for 15 years. General Naga sends his wife, Lady Naga, formerly known as Doctor Zero, to engage in peace talks with the Anti-Traction nation of Zagwa, which had previously rejected the Green Storm’s extremist ideology of total war against the Traction Cities.
Theo is flying a one-person kite when he sees an air fleet of Super-Gnats, fighter-bomber ships from the Traction Cities of the Traktionstadtsgesellschaft, approaching Zagwa. He deduces that they’re coming to violate the truce and bomb Zagwa. Theo abandons his kite and invades a Super-Gnat, sending a radio message to Zagwa that they’re being attacked.
Theo is wounded while saving the city from attack, and Lady Naga operates on him to save his life. He learns from her that the attack was actually perpetrated by the Green Storm, some of whom hate Lady Naga for influencing General Naga to pursue peace.
Wren and her father, Tom, are flying their airship, the Jenny Haniver, through the Bird Roads. Tom’s health is failing because of an old bullet wound near his heart. He is also sorrowful because his wife, Hester, ran away and abandoned him and Wren after the battle of Brighton. In Peripatetiapolis, Tom sees a woman he knew from his youth in London, which lets him know that London wasn’t truly destroyed. He resolves to follow his curiosity and look for more information about London.
In Cairo, the little boy Fishcake is living with Stalker Fang, whom he repaired after she was nearly destroyed in Brighton. The Stalker has a split personality: Anna, who is kind and motherly to Fishcake, and Stalker Fang, who wants to regain power and destroy all Traction Cities. They steal a limpet ship from Brighton and reach Shan Guo, stopping to rest at a hermitage on the inactive volcano of Zhan Shan.
At the hermitage, Anna is surprised to find her old mentee, Sathya, not remembering that the Stalker Fang cut off Sathya’s arm and left her for dead. Fishcake hopes the presence of Anna’s old friend will make the Anna side win out permanently over the murderous Stalker Fang side.
Theo goes on an airship mission to guard Lady Naga and deliver her safely to General Naga in Tienjing, but their ship is sabotaged by a spy. After the ship’s crash, a slaver kidnaps Lady Naga. Hester and Stalker Shrike, who have been traveling together, rescue Theo from the engine pits of Cutler's Gap. Shrike was rebuilt by Lady Naga, who programmed him to be incapable of killing anyone, but Hester has no such limits and has been making her living as an assassin.
Tom and Wren go to Murnau and meet Professor Pennyroyal, the man who shot Tom 20 years ago but who has since become a sort of friend to the Natsworthys. When Tom tries to get information about the wreck of old London, Pennyroyal says London is haunted; no one goes there anymore. Wolf Kobold, son of Murnau’s mayor, is interested in the Natsworthys. They join him aboard his burrowing suburb of Harrowbarrow on a mission to explore the ruins of London.
Fishcake and Stalker Fang leave Sathya’s peaceful hermitage and travel to Batmunkh Gompa to meet Stalker Fang’s maker, Dr. Popjoy. Anna wants Dr. Popjoy to permanently dampen her Fang side, but Stalker Fang takes over their shared body, kills Dr. Popjoy and leaves Batmunkh Gompa with Fishcake in Dr. Popjoy’s air-yacht. They go to Anna’s old home of Erdene Tezh so that she can contact ODIN, an ancient orbital weapon of mass destruction.
In the wreck of London, Tom, Wren and Wolf are taken prisoner by the Londoners, whose mayor is Chudleigh Pomeroy, Tom’s former boss. London is building the small hovering city of New London, which they hope will float on magnetic currents and carry them to a better life. Wolf runs away to find his nearby suburb of Harrowbarrow so he can attack New London and use its technology to help his own suburb.
Hester, Shrike and Theo come to Airhaven in the airship Shadow Aspect and try to buy Lady Naga from a slaver named Varley. They don’t have enough money, but when they encounter a disguised Pennyroyal walking in Airhaven, Hester robs him and returns to Varley. She gets into a fight with Varley, but just as Varley is about to kill Hester, his own wife shoots him first.
Wolf’s father, a good mayor named von Kobold, arrives to help Hester, who is bleeding from a head wound, and Lady Naga. Pennyroyal and some men from Manchester face off against von Kobold in an attempt to kidnap Lady Naga, but instead Shrike takes Lady Naga and Hester back to the Shadow Aspect where Theo flies them to safety.
Lady Naga treats Hester’s wound and makes contact with the Green Storm, who gives them coordinates to an airfield where they can land. Shrike discovers Pennyroyal clinging to the Shadow Aspect’s tailfin and brings him aboard. Pennyroyal gives Theo a letter from Wren, which lets him know she has gone to London.
The Traktionstadtsgesellschaft mobilize to attack the border line of the Green Storm’s territory. General Naga, saddened by his wife’s supposed death and weakened by poison from a spy loyal to Stalker Fang, doesn’t respond to mobilize the Green Storm troops in return. The Traktionstadtsgesellschaft attack the airfield where Lady Naga is, but she, Hester and Shrike escape to the Green Storm’s Forward Command where Hester remains unconscious for a few days, recovering from her wound.
When Hester wakes up and finds that Theo was left behind on the airfield during the attack, she assumes he is dead and feels heartbroken. In the newly restarted war, the Traktionstadtsgesellschaft are winning handily against the Green Storm until several Traction Cities are destroyed by ODIN, which fires on them from orbit at Stalker Fang’s command. ODIN also destroys Tienjing, the Anti-Tractionist headquarters, but General Naga survives.
Theo travels to London on foot to find Wren. When they are reunited, he tells her that her mom, Hester, is traveling with Shrike and that Hester is a brave, tough person. Wren doesn’t know how to feel about her mother since she ran away after the battle of Brighton, but she is glad to see Theo again and they begin a romantic relationship.
Seeing ODIN firing upon distant cities and hoping to protect Wren, Tom decides to fly the Jenny Haniver to Batmunkh Gompa to talk with General Naga and convince him not to attack New London. General Naga does not believe that Tom is really from London, and instead believes he’s a Tractionist agent. Wren and Theo have to escape from London when they are accused of being Green Storm members.
Hester, Shrike, Pennyroyal and Lady Naga reach Batmunkh Gompa, where they hear that Tienjing and several Traction Cities have been destroyed. Shrike guesses that Stalker Fang is firing on both armies in order to sow confusion. General Naga is not happy to see Lady Naga and blames her for Tienjing’s destruction because he thinks it is London attacking the Anti-Tractionists, not Stalker Fang. Hester reunites with Tom, and they both watch as ODIN fires on the volcano of Zhan Shan, causing it to erupt.
Wren sees the burrowing suburb of Harrowbarrow returning to attack London, so she intentionally lets herself get captured by Harrowbarrow. She feigns friendliness toward Wolf and leads his city into a damaging electricity field, though the suburb continues its advance toward London. Theo joins her. General Naga flies to London, but discovers that the Londoners are not controlling ODIN’s power. Naga tells the London engineers to start flying their new city so that they can escape the oncoming Harrowbarrow.
Tom, Hester and Shrike take the Jenny Haniver to Erdene Tezh with Pennyroyal as a stowaway, but the Jenny Haniver crashes. When they approach Anna’s old house, Fishcake attacks Hester, because he once vowed to kill her. Stalker Fang doesn’t allow him to continue attacking them because she has fond memories of Hester and Tom.
Tom faints from his heart condition, and Stalker Fang lets him rest because she knows he’s dying. She explains to him that she means to use ODIN to ignite volcanoes all over the earth, destroying all life so that the earth can heal itself from the plague of human cities, both Traction and Anti-Traction.
As Harrowbarrow pursues the fast-floating New London, Wren and Theo fight Wolf. An accident causes Wolf to impale himself on Wren’s weapon, killing him. General Naga rescues Wren and Theo from Harrowbarrow and deposits them on New London. General Naga then flies his airship solo and kamikaze-bombs Harrowbarrow so that New London can escape.
At Erdene Tezh, Tom begs Stalker Fang to destroy ODIN so that Wren can live. Stalker Fang enters a command into ODIN’s transmitter, and then Pennyroyal arrives and kills Stalker Fang with a lightning gun, destroying the machinery of ODIN’s transmitter in the process.
In the night sky, Tom and Hester see an explosion of light, which they know is ODIN blowing itself up from Stalker Fang’s command. Tom collapses in pain. Pennyroyal goes to bring a ship to rescue Tom and Hester, but Fishcake threatens him with a knife and forces him to abandon them, just as they once abandoned him.
In Batmunkh Gompa, the remaining Green Storm troops see ODIN disintegrating and promote Lady Naga as the new leader of the Anti-Traction League, since she is wise and peaceful and the whole world is in turmoil. In the wake of ODIN’s destruction, many Traction Cities become static and work in cooperation with the Anti-Tractionists.
Fishcake walks back to the hermitage at Zhan Shan and grows up in Sathya’s house, eventually becoming a successful adult and having children of his own. Wren and Theo go to Zagwa, where his family welcomes Wren and their plans to marry. Wren and Theo purchase an airship they name the Jenny Haniver II, and they intend to become air-traders, shuttling back and forth between New London and the many cities that are safe to visit during the new era of peace.
After Stalker Fang’s death, Shrike runs to Erdene Tezh to rescue Hester and Tom, but discovers that Tom has died of heart failure and Hester has committed suicide by stabbing herself in the heart. Stalker lays their bodies under an oak sapling and sits unmoving as they decompose over the years.
In a dreamlike state, Shrike waits for hundreds of years until he sees children. He wakes himself up and discovers that the children have been decking him with garlands of flowers. The children lead him down to their village, and the peaceful happy villagers no longer remember an era when there were Traction Cities. People ask what his function is and he tells them he is a Remembering Machine. The townspeople ask him to tell a story, so he begins to narrate the story of Tom and Hester, beginning with the opening paragraph of Mortal Engines, the first book in the series.