The book is set six months after Infernal Devices. Wren Natsworthy and her father Tom Natsworthy have taken to the skies in their airship, the Jenny Haniver. After the apparent death of the Stalker Fang at the end of Infernal Devices, General Naga has seized command of the Green Storm and has signed a peace treaty between the Green Storm and the Traktionstadtsgesellschaft, ushering in a new era of peace and trade. Whilst Wren is enjoying life as an aviator, Tom misses Hester, and has been informed by a doctor that his weak heart means he only has a few years left to live. The Lost Boy, Fishcake, is secretly repairing the Stalker Fang, coming to regard her as the mother he never had. Theo Ngoni has returned to Zagwa and rejoined his family.
The title is derived from Matthew Arnold's poem Dover Beach. This excerpt of the poem appears at the beginning of the book:
Ah, love, let us be true
To one another! for the world, which seems
To lie before us like a land of dreams,
So various, so beautiful so new,
Hath really neither joy, nor love, nor light,
Nor certitude, nor peace, nor help for pain;
And we are here as on a darkling plain
Swept with confused alarms of struggle and flight
Where ignorant armies clash by night.
This relates to the novel in several ways. The characters are indeed swept about, often against their will, by the "ignorant armies" of the Green Storm and Traktionstadtsgesellschaft, on the "darkling plain" of the Great Hunting Ground.
Reeve references his choice of title himself towards the end of the book when the character Nimrod Pennyroyal writes a book within a book titled Ignorant Armies.
The similarly titled, "As on a Darkling Plain", by Ben Bova in 1972 also takes its title from this poem.
Theo Ngoni, having returned to his family in Zagwa, foils an attempt to assassinate Oenone Zero, who has married General Naga and has taken the title of Lady Naga. Oenone suspects that the assassination attempt was organized by factions in the Green Storm still loyal to the Stalker Fang.
The Stalker Fang, rebuilt by Fishcake, is demanding that he return to Shan Guo so that she can activate ODIN. They steal a limpet from Brighton (now ruled by warring gangs of Lost Boys) and go to the volcano of Zhan Shan in Central Asia. The general despairs and Twite becomes his servant so that she can infiltrate his government and topple it from within. In the ruins of London, Wren and Wolf discover a new city called "New London": built to float above the ground by magnetic levitation technology. Wolf escapes from London with this knowledge, intending to return and devour the new city with Harrowbarrow.
Napster Varley arrives in Airhaven, which is floating above the Traktionstadtsgesellschaft, and makes cautious attempts to sell Oenone. Hester, Theo, and Shrike attempt to buy her back, but they do not have enough money. Hester then finds Pennyroyal hiding in Airhaven, in disgrace and debt after a newspaper exposed him as a fraud. She takes what remains of his money and heads to Varley's ship to buy Oenone. Pennyroyal rounds up troops from Manchester to try to get there first.
Hester attempts to cheat Varley, but is discovered and has to fight her way out. Varley is killed by his wife and she escapes with Oenone when Pennyroyal and his troops challenge them. A fight ensues, and in the confusion Hester and her party escape on their airship. Pennyroyal falls from Airhaven and is assumed killed, but lands in the rigging of Hester's airship. The five of them make it across no-man's land to a Green Storm airbase, where they are hailed as heroes. The airbase is soon attacked by the Traktionstadtsgesellschaft. All escape in an airship heading east except Theo. Meanwhile, the Stalker Fang and Fishcake arrive in Erdene Tezh, her old home. She begins to assemble a powerful radio station to send a signal to ODIN.
Theo survives the attack on the airfield and treks east across the plains in search of Wren. He is welcomed into the ruins of London by the community there and reunited with Wren, but brings bad news that the war has started again. The development of New London is pushed faster. The Stalker Fang has activated ODIN and turns it on the Traktionstadtsgesellschaft. Manchester and many other cities are destroyed, and the surviving cities flee west. In Tienjing, news of Oenone's survival reaches General Naga. He realises Cynthia Twite had deceived him and confronts her. She is about to kill him when ODIN fires upon the city. Twite is killed instantly but Naga survives. He takes the shattered remnants of his government and flees to Batmunkh Gompa. News of ODIN's destruction reaches the ruins of London, where the citizens assume it is a new weapon of Naga's. Tom decides to take the Jenny Haniver east to convince the General to not destroy New London, as it will not damage the earth as the other Traction Cities do. He sneaks away in the dead of night, leaving a letter for Wren. In no-man's land, news comes to Harrowbarrow of the destruction of the Traktionstadtsgesellschaft. Wolf is determined to carry on to the ruins of London, and tells his second-in-command that after the Sixty Minute War, the creatures that survived best were cockroaches and rats. He believes that with the old cities gone, the time for creeping places like Harrowbarrow is at hand, and they continue east.
On the same night that Tom slipped away, Chudleigh Pomeroy died in his sleep. He is succeeded by Mr. Garamond, the paranoid head of security who is convinced that Tom has gone to tell the cities about New London and that Wren and Theo are traitors. The airship is attacked by Stalker-birds. Shrike defends the ship but falls from it, into the mountains. The Jenny Haniver then crashes on the shores of the lake at Erdene Tezh, and the three escape as it burns. Theo and Wren are engaged in a sword fight with Wolf on top of Harrowbarrow, as New London flees. Wren accidentally kills Wolf and they are rescued by General Naga, who takes them back to New London. Harrowbarrow continues to pursue the young city, and the General sacrifices himself in a kamikaze attack, whereupon New London escapes across the plains.
Tom and Hester arrive at Stalker Fang's location, and convince her to deactivate and destroy ODIN. Tom soon dies of his heart disease, and Hester commits suicide. Shrike finds them both dead, and begins to shut down. After a long time, Shrike is reactivated by villagers. The villagers take him to the town hall and ask if he is one of the machine men out of stories they have heard. Shrike tells them he is a "Remembering Machine" and narrates his story, beginning with the first line of Mortal Engines.