The novel begins on the planet of Arrakis, 35 years before the events of the original Dune. The Baron Vladimir Harkonnen has just taken over the governorship of Arrakis (also called Dune) from his younger brother Abulurd, who has allowed spice production to decrease heavily. The Baron sees an opportunity for large profits and begins to store up illegal spice hoards.
On the Imperial Capital planet Kaitain, the young planetologist Pardot Kynes has just arrived from his homeworld of Salusa Secundus for an audience with the Padishah Emperor, his majesty Elrood Corrino IX. The old Emperor is giving Kynes the mission of going to the only known source of melange, Arrakis, in order to find out how the precious substance is produced. Meanwhile, the Crown Prince Shaddam and his minion Hasimir Fenring are plotting against Elrood. Shaddam is not getting any younger, and it seems that the already 157-year-old Emperor could rule for another 50 years. Shaddam decides to poison his father in order to speed up his succession to the throne.
Duke Paulus Atreides in the duchy of Caladan is planning on sending his young son and heir Leto to the court of Earl Dominic Vernius on Ix in order to study politics with the Earl's son Rhombur. Leto's mother, the Lady Helena, does not like the idea. Not only is she a very religious woman, but her father is also the Count Richese, who is the main rival of the Earl Vernius.
The Bene Gesserit are getting closer to their quest to breed the Kwisatz Haderach; only three generations remain. The next step is to send the Reverend Mother Gaius Helen Mohiam to Giedi Prime, the Harkonnen home world, in order to conceive a child with the Baron Vladimir. This child would in turn be married to Leto Atreides to produce the eventual mother of the Kwisatz Haderach. The Baron is initially not interested, but after being blackmailed with the secret of his spice hoards, he has sex with Mohiam and a daughter is conceived.
Meanwhile, the young Harkonnen slave boy no. 11368, Duncan Idaho, is trying to escape the forests of Giedi Prime, where the na-baron Glossu Rabban is trying to kill him as a part of a game he and his friends are playing. Duncan finally manages to escape the planet, boarding a heighliner en route to Caladan.
