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Twelve years after the emperor's death, the Fremen armies have successfully subdued all known planets, killing off millions in numerous battles. The desert plant Arrakis 'Dune' has become an imperial capital, still thanks to its monopoly on the spice. Now Paul Muad'Dib Atreidis' son and daughter are coming of age, the stage is set for a new power game. The spice guilt has prepared a secret weapon: perfect clones. A reconstructed Duncan Idaho is offered to and accepted as a gift by the reigning Atreides, although Stilgar warns against the sisterhood's crafty power-hunger.

As conspiracies to gain political power abound, Paul's power base is eroded from within and his highly ambitious sister, Alia is gaining a political foothold. Born aware of her ancestral memories, Alia is considered an abomination by the Bene Gesserit. The Lady Jessica, her mother returns to Dune (Arrakis) to visit her grandchildren Leto II and Ghanima. When one particular ancestor begins to possess Alia, Lady Jessica has to take refuge. Leto II and Ghanima devise a plan toward salvation.

As Alia becomes totally possessed she also has to deal with rebel Fremen. Ghanima, who survived an attack on her by House Corrino, is now engaged to Farad'n Corrino. Unexpectedly, Leto II returns from the desert being believed dead. While in the desert his body has absorbed some sand-trout, slowly mutating him into a sand-worm. Alia resists possession by the baron while Irulan declines Jessica's offer to return with her to Caladan.