Several months have passed since the events of the first novel. Gregor is determined to never go back to the Underland, but another prophecy by Bartholomew of Sandwich predicts otherwise, and so the Underlanders bring him and his sister back down through an entrance to their world located in Central Park. Once below, Gregor learns of "The Prophecy of Bane", which the Underlanders interpret to mean that he must kill a white rat (known as the Bane) of whom they have just received intelligence. Historically, enormous white-coated rats have appeared below every few centuries and caused havoc for the humans, so the Underlanders train Gregor briefly then send him off to a place known as the Labyrinth where the Bane is in hiding.
The quest group undergoes several difficulties, including being caught in a whirlpool, encountering an island of carnivorous insects, and being betrayed by two shiners (fireflies) who were hired to provide them with light. Gregor himself begins to struggle with a new "power" that manifests when he is in battle. He is what the Underland creatures call a rager, a person who is overcome by a kind of "battle-fury" when they fight, making them completely deadly even without training. Gregor and his bond Ares's worst trouble, however, is when they and the remaining questers become separated from Luxa, Temp, and Boots during a fight with some serpents. The three missing are assumed dead, and Gregor finds himself emotionally frozen at the thought of having lost his baby sister.
When he finally finds the Bane, he learns that it is not an adult monster, as was assumed, but instead a small baby whose parents have just been killed. He can not bring himself to kill it, and so he and Ares take it to be raised by the only friendly rat they know: Ripred. After this, the two return to Regalia, where Nerissa has just been crowned queen due to the crown princess's apparent death. The flier Andromeda, human Howard, Ares, and Gregor are tried for treason because they failed to kill the Bane. They are saved, though, by Nerissa, who explains how it is good Gregor was not heartless enough to kill a baby. Shortly thereafter, Gregor is trying to finally face the reality of going home without Boots when she is suddenly returned to the palace, having been saved in turn by Luxa, Temp, and an unnamed moth. The two then return to the surface world.
If Under fell, if Over leaped,
If life was death, if death life reaped,
Something rises from the gloom
To make the Underland a tomb.
Meaning: These lines are a reference to the first prophecy, and essentially state that if Henry died and Gregor lived, then a new danger to the Underland will rise.
Hear it scratching down below,
Rat of long-forgotten snow,
Evil cloaked in coat of white
Will the warrior drain your light?
Meaning: This stanza refers to the rat called the Bane, who is hidden from most of the Underland. Banes are traditionally white-colored, like snow, and highly dangerous. The author, Sandwich, poses the question of whether Gregor (the warrior) will kill this rat, using an Underland idiom for "life".
What could turn the warrior weak?
What do burning gnawers seek?
Just a barely speaking pup
Who holds the land of Under up.
Meaning: These lines are the most ambiguous of the prophecy. They are first assumed to be about Boots, though the Underlanders later concede they could have also been partially or wholly about the baby Bane. Both are barely speaking pups, or children, and are important to the Underland. Both could also "turn the warrior weak", Boots by dying and leaving Gregor heartbroken, and the Bane by surprising Gregor (for being a child).
Die the baby, die his heart,
Die his most essential part.
Die the peace that rules the hour.
Gnawers have their key to power
Meaning: Many Underlanders believe these lines refer to the death of Boots, because it would surely crush Gregor and make him useless to them as a warrior. Gregor and Nerissa, however, postulate that Gregor's hypothetical murder of the baby Bane would have been equally disastrous because it would have destroyed his humanity. This could have made him emotionally unstable, and the Bane's death would have inflamed the rats and destroyed their fragile peace with the humans.Gregor: An eleven-year-old Overlander, said to be the warrior mentioned in "The Prophecy of Bane".
Boots (Margaret): Boots is Gregor's two-year-old sister. She is known as "the princess" by the crawlers.
Howard: Luxa's cousin, brought along for his skills in water aid. He is bonded to Pandora.
Mareth: A soldier and friend of Gregor, severely injured during the fight with the serpents. He is bonded to Andromeda.
Twitchtip: A gnawer (rat) Ripred sends along because of her incredible sense of smell; she is an outcast and "scent-seer".
Temp: A crawler and friend of Boots. He is lost during the battle with the serpents, then later loses a few legs while escaping some rats with Boots. He remains behind to regrow them while she is sent ahead.
Photos Glow-Glow and Zap: Two hired fireflies who desert the quest and inform the rats of the quest's approach when their pay (large quantities of food) runs out.
Ares: A large black flier (bat) bonded to Gregor. He is extremely strong, and similar to Gregor in many ways; the two become friends.
Pandora: Howard's bond, eaten alive by carnivorous mites.
Andromeda: Mareth's bond.
Aurora: Not technically part of the quest, Aurora is bonded to Luxa and accompanies her to join the quest after the boats carrying the members are too far from land for them to be sent home. She is lost and presumed dead after the battle with the serpents.
Luxa: The rebellious future queen of Regalia. She is not officially a quest member as she joins after they have already set out, and is lost with Aurora after the battle with the serpents.
Scholastic has licensed rights to publish in 20 different languages. To date, editions have been published in Italian, Turkish, German, Portuguese, Bulgarian, Finnish, Spanish, Danish, Dutch, Swedish, French, Greek, Norwegian, Polish, Persian, and Chinese. Several foreign-language editions possess unique cover art. Many have unique titles as well, such as the Dutch Het Labyrint ("The Labyrinth") and Portuguese Gregor e a Segunda Profecia ("Gregor and the Second Prophecy").
The novel has also been released in ebook and audiobook form. Multiple editions have been published in most languages; for example, audiobooks, paperbacks, and hardcovers have been published in English, German, and Spanish.
Like the first book, Prophecy of Bane received critical acclaim, especially for its treatment of difficult issues in a way that is accessible for young readers. April Irick, an Amazon Book Critic, gave the following review: "The stories are dark... almost constant action. The dialogue is also great." Carl E. Ahlm, also of Amazon, said, "I am impressed by the themes that are evolving in these books: violence and war, the lust for power, conflicts between 'groups' who are 'different,' and thus, it speaks to tolerance. Collins fills the reader with angst, as the book is filled with intense emotions: deaths, traps, threats, betrayal, frustration, questionable alliances, compassion, and cruelty." Geek Girls praised the novel in a similar way, stating that "The world that Collins has created is amazing. She has managed to weave a tale in which creatures that are classically seen as evil or disgusting (rats, spiders, bats, etc.) are seen as friends. Not an easy feat."
Several critics have lauded the novel specifically as a sequel to the first book of the Underland Chronicles. For example, the book's Booklist review claimed "...fans will not be disappointed with this exciting, action-packed sequel, whose ending suggests more adventures to come." The Horn Book Magazine similarly stated, "Along with many Underlanders (rats notwithstanding), Gregor’s fans will cheer the promise of future visits." The story has also received positive reviews for its quality as a fantasy novel. School Library Journal said, "This is a strong choice for fantasy fans, including reluctant readers, even if they're not familiar with Gregor's first adventure."
Gregor and the Prophecy of Bane is a New York Times Bestseller; Book Sense Bestseller and Children's Pick; and Connecticut Book Award Finalist (2005).