In a parallel universe, England and Imperial Russia have fought the Crimean War for more than a century; England itself is still a parliamentary government, although heavily influenced by the Goliath Corporation (a powerful weapon-producing company with questionable morals); and Wales is a separate, socialist nation. The book's fictional version of Jane Eyre ends with Jane accompanying her cousin, St. John Rivers, to India in order to help him with his missionary work. Literary questions (especially the question of Shakespearean authorship) are debated so hotly that they sometimes inspire gang wars and murder. While regular law enforcement agencies still exist, new have also been created to deal with situations too specialized for the traditional ones. These agencies fall under the single organization SpecOps (Special Operations), with more than 20 branches, including SpecOps 12, the Chronoguard, who police all events related to Time travel, and SpecOps 27, the Literary Detectives, or "LiteraTecs", who deal with all literature-related crimes.
While the Crimean War has continued, outright battle has been avoided for several years, as both sides are at a stalemate. The war is now fought due to principle, with both sides being too stubborn to call for peace, and the Crimea has been so devastated by over 100 years of war that it is of no use to either side. There is also a peace movement in Britain which is gaining ground in popularity. Meanwhile, Goliath has been contracted to create a new type of handheld weapon, a plasma rifle codenamed "STONK", which threatens to reignite bloodshed, as the Russians have no equivalent, and the weapon is capable of destroying a tank with a single blast. Goliath promises that STONK will soon be standard issue to the British Military.
Single, thirty-six-year-old, Crimean War veteran and literary detective Thursday Next lives in London with her pet dodo, Pickwick. She is privately against the continuation of the war, as her brother was killed in action and her then fiancé Landen Parke-Laine lost a leg in combat. The trauma of the war led to the end of her relationship with Park-Laine several years prior.
As the story begins, Thursday is temporarily promoted to assist in the capture of a wanted terrorist, her former university professor, Acheron Hades, a mysterious criminal mastermind who has no photos of himself on police record. Thursday is therefore one of the only living people who can recognize him. She comes close to capturing him during a stakeout. However, unknown to them, Hades possesses several superhuman abilities, such as mental manipulation and extreme durability. He therefore is able to withstand their gunfire and escapes, killing Thursday's entire team, and she is shot. She is saved by a copy of Jane Eyre that stops Hades' bullet. A mysterious stranger aids her until the paramedics arrive, leaving behind only a handkerchief monogrammed with the letters "E.F.R." and a 19th-century style jacket. Next recognizes these items as these as belonging to Edward Fairfax Rochester, a fictional character from Jane Eyre. As a child, Thursday had experienced a seemingly supernatural event, whereby she was able to physically enter the world of the novel and briefly became acquainted with Rochester himself while she was there.
While recovering in hospital, she learns that, after fleeing the scene, Hades was seemingly killed in a car accident. She also meets a time traveling future-version of herself, who warns her that Hades survived the accident, and instructs her to take a LiteraTec job in her home town of Swindon, which she does. There, while visiting her family, she discovers that her brilliant Uncle Mycroft and Aunt Polly have created the Prose Portal, a device which allows people to enter works of fiction. Next also renews an acquaintance with Parke-Laine. She also meets, and is forced to work with, a high ranking Goliath Operative named Jack Schitt, who is also investigating Hades, although he refuses to reveal why.
Hades, meanwhile, steals the original manuscript of Charles Dickens's Martin Chuzzlewit. He also kidnaps Mycroft, Polly, and the Prose Portal in order to blackmail the literary world; any changes made to the plot of a novel's original manuscript will change all other copies. To demonstrate his demands are serious, Hades kills Mr Quaverley, a minor character from the original manuscript of Martin Chuzzlewit. When his demands are not met he also stages a theft of the original manuscript of "Jane Eyre", and kidnaps Jane for another ransom demand. This causes the text of all copies of the Jane Eyre novel to abruptly end at the moment of Jane's kidnapping, roughly halfway through the book.
Next and Jack Schitt independently trace Hades to Wales, and she rescues Mycroft and the Prose Portal, and returns Jane to the novel. However, she finds that Polly is stuck in one of Wordsworth's poems and Hades has gone into the original text of Jane Eyre carrying the scrap of paper Polly is imprisoned on. Next is forced to pursue Hades, and after several weeks in the novel (which pass in the outside world much more quickly, as the book rewrites itself after Jane is returned) and much trouble, succeeds in killing him and recovering the poem Polly is held on. In the process, Thornfield Hall is burned, Rochester's mad wife Bertha falls to her death, and Rochester himself is grievously injured. Thursday also discovers that the characters in the book must continually relive their lives, with full knowledge of how events turn out, and are unable to alter any of them, meaning that Rochester must continually experience the devastating loss of Jane when she runs away from him upon discovering his secret marriage. Thursday, who has befriended Rochester, resolves to change the ending of the book to a happy one, and is able to change events to reunite Jane and Rochester (in other words, she alters the ending of the book to match the actual ending to Jane Eyre).
Returning to her own world, Next uses the Prose Portal to release her Aunt Polly. Jack Schitt reveals that his interest is actually in the Prose Portal. Goliath had never actually been able to perfect STONK into a feasible weapon. Therefore, with their deadline to deliver the weapons to the military, had resolved to use the Prose Portal to extract working STONKs from the weapon's manual, itself a work of fiction, as the weapons don't work. Thursday reluctantly agrees to let Schitt use the portal for this endeavor, but switches the book connected to the portal to be the text of Edgar Allan Poe's "The Raven". When the portal opens, she pushes Schitt inside, and traps him there, while Mycroft destroys the portal.
Using her new celebrity status, she enters a televised debate between supporters and opponents of the continuation of the Crimean War. Supporters of the war assume that Goliath's plasma rifles will be sufficient to guarantee victory. But in the debate, Next publicly reveals to the world that the plasma rifles do not work. This forces England to rethink its position, which leads to actual peace negotiations, which effectively end the war.
She shows up at the church where Parke-Laine is about to be married to another woman, but Rochester's lawyer interrupts the wedding and Next and Parke-Laine are reconciled and marry instead. Next's father, a renegade agent from SpecOps-12, the ChronoGuard, turns up to dispense some fatherly advice to his daughter. The novel ends with Next facing an uncertain future at work: public reaction to the new ending for Jane Eyre is positive, but there are other repercussions, including Goliath's fury.