"The Well of Lost Plots" is the third book in the ongoing series by Jasper Fforde. It centers around the protagonist, literary detective Thursday Next, who is the narrator.

Thursday is an operative with SpeOps-27 in the real world, but as "The Well of Lost Plots" opens, she is taking a much-needed vacation inside the BookWorld. She is pregnant by her husband, Landen Parke-Laine, who was eradicated in the real world and exists only in her memories. Aornis Hades, an enemy from a previous book, infiltrates Thursday as a mindworm, trying to get her to forget her husband. If Thursday forgets him, there is no hope of his return to the real world.

Thursday is in the BookWorld as part of the Character Exchange Program in the unpublished novel Caversham Heights. It is an unpublished book, and the protagonist, DCI Jack Spratt is afraid it will be disassembled. He hopes to use Thursday's influence in the BookWorld to appeal to the Council of Genres to prevent it from happening.

While in the BookWorld, Thursday is continuing her apprenticeship into Jurisfiction under the guidance of Miss Havisham of Great Expectations. Jurisfiction is on edge because Yorrick Kaine, a fictional character, has escaped into the Outland, while an Outlander is in the BookWorld and has teamed up with Kaine and Text Grand Central to release BOOK v.9, code-named UltraWord.

Living with Thursday in Caversham Heights are two Generics from St. Tabularasa's, Ibb and Obb. They are undergoing training to become characters, and be assigned books. As they go through training, they begin to develop distinct personalities, which Thursday likens to going through puberty.

The Minotaur escapes, killing Perkins and Mathias. Snell is killed by a mispeling vyrus. After Thursday is sworn in as a full agent, Miss Havisham and Thursday are looking into the deaths when Miss Havisham is killed as a result of an accident during a land speed attempt in the Outland. Just before she dies, Miss Havisham gives Thursday an UltraWord(TM) copy of The Little Prince she had been testing, and tells her the formulaic is the enemy.

Thursday battles Aornis's mindworm in a final nightmare and is victorious, gaining her memories back, particularly of Landen. Thursday is assigned to work with Solomon, essentially as a bailiff. More of the witches' prophecy comes true.

Thursday decodes Snell's nonsense message and Tweed reveals himself as the murderer of Perkins. When he accuses Thursday of killing Perkins with the motive of becoming the Bellman, Deane helps Thursday escape her arrest, and the two of them come up with a plan to keep UltraWord(TM) from being voted in at the BookAwards. They cut Tweed off from Text Grand Central, and Thursday explains the problems with UltraWord(TM). However, Tweed gets the connection back and the Bellman is calling for a vote, so Thursday pulls the emergency lever in her TravelBook.

The Great Panjandrum appears and freezes all the text in the room, calling for a vote right then, which votes down UltraWord(TM). The Great Panjandrum also appoints Thursday to be the next Bellman. Thursday saves Lola from being auctioned, reuniting her with Randolph, then saves Caversham Heights by setting it up as a sanctuary for worn out characters, which also ends the nursery rhyme characters' strike.

The final chapter is exclusive to the U.S. Edition of "The Well of Lost Plots", and describes how Thursday handles a WordStorm in the BookWorld.