The Eyre Affair is a unique detective novel by Welsh writer, Jasper Fforde. In this novel, Thursday Next is a detective with SO-27, the LiteraTec division. Thursday's job is to solve crimes related to literature. When the original manuscript of Martin Chuzzlewit by Charles Dickens disappears under impossible circumstances, Thursday finds herself drawn into an investigation that is more deadly than anything she has experienced thus far in her career. Thursday finds herself on the track of Acheron Hades, a one-time college professor who is now a criminal with powers beyond even Thursday's experiences. When the investigation brings Thursday home, she must face not only the nightmares of Hades, but the nightmares of her own past as well. The Eyre Affair is a detective novel that is both fantastical in its altered reality and all too real in its heroine's struggles.

Thursday Next gets word that the original manuscript of Martin Chuzzlewit by Charles Dickens has disappeared from the Dickens' Museum, despite the fact that she designed its security herself. Thursday is baffled by the case until she is approached by Tamworth from SO-5. Tamworth suggests that the manuscript was taken by Acheron Hades, a criminal mastermind with powers almost unimaginable. Thursday can identify Hades because he was once one of her college professors, so Tamworth asks Thursday to join SO-5 until Hades can be apprehended. Thursday quickly agrees as this is a big step up in her career.

Thursday waits weeks before receiving the call from Tamworth. When she does, Thursday identifies Hades as he enters his brother's apartment. Thursday and Tamworth storm the apartment, but Hades is ready for them. Hades kills Tamworth and runs away despite the multiple bullets Thursday shoots into him. Thursday follows Hades outside the apartment building where she discovers he had killed another of Tamworth's men. Thursday confronts Hades and he shoots her, leaving her for dead in the street. If not for a mysterious man, Thursday might have bled to death.

After telling her story to SO-1, and leaving with the feeling that they do not believe anything she has said, Thursday returns to her room where she encounters herself from the future. This future Thursday tells her to take a LiteraTec job in Swindon, her home town. When Thursday leaves the hospital and is given her things, she finds evidence of the mystery man's identity. It seems Edward Rochester stepped out of the pages of Jane Eyre to save her life. This is not the first time Thursday had met Mr. Rochester. When Thursday was a small child, she went to Haworth, where she stepped into the novel herself and caused Rochester's horse to trip the day he met Jane at the stile.

Thursday returns to her hometown of Swindon, where she takes up the job with LiteraTec. Thursday immediately begins searching for Hades while at the same time dealing with her past. Thursday's ex-fiance still lives in Swindon. He comes to see her at the hotel. Thursday is shocked by her strong reaction to him, but discovers that she still cannot forgive him for turning on her brother in an inquest regarding the ambush that killed Anton Next and nearly killed both Thursday and her ex-fiance.

Thursday's uncle, an inventor, has created a Prose Portal that allows him to open a doorway into literature. On the morning Uncle Mycroft tries out the portal with his wife, Polly, Hades comes to steal the portal. Polly is trapped in a Wordsworth poem, forcing Mycroft to help Hades steal a minor character from Martin Chuzzlewit. A few days later, Thursday witnesses the character's autopsy. Hades then makes a demand for money in exchange for the life of Martin Chuzzlewit. The SpecOps makes a drop, but the money is fake. However, Mycroft has burned the manuscript of Chuzzlewit, barring Hades from killing anymore characters.

Hades steals the original manuscript of Jane Eyre from Haworth. Hades kidnaps Jane from the pages of the book in the part where Jane saves Mr. Rochester from a fire. The narration is first person, therefore the book ends at that point without Jane to narrate. Thursday figures out where Hades is hiding and rushes there to save her uncle and her favorite book. Thursday manages to get back into Jane Eyre with Jane in tow, but Hades has followed. Thursday must wait till the end of the book, out of sight of Jane to prevent changes to the narration. At the end of the book, Hades confronts Thursday in an attempt to get her password to leave the book. Thursday refuses to give it and a fight breaks out. Soon Thornfield catches fire. Mr. Rochester is crippled and blinded while attempting to help Thursday. Hades kills Mrs. Rochester, but Thursday finally figures out how to kill Hades.

While waiting to find a way to escape from the book, Thursday changes the ending of the book by whispering Jane's name outside her window, causing her to come to Thornfield one last time. Jane sees Mr. Rochester and decides to marry him now that his wife is dead, despite his injuries. Jane and Roccester live ten happy years in this new ending of the book. Thursday, in the meantime, returns to her own reality in time to stop her ex-fiance's wedding. However, when she arrives, Thursday loses her nerve and is unable to stop the wedding. The lawyer from Jane Eyre arrives just in the nick of time and stops the wedding by revealing that the bride is already married to someone else. Thursday and her ex-fiance get married a month later.