The novel consists of several different plot lines, which, while they interact with one another at certain points, are best described separately.
- Spoiler warning! Plot and/or ending details follow.
Shaddam IV finally sits upon the Golden Lion Throne, enjoying his position as ruler of the Known Universe. However, his rule as Emperor is precarious at best, as his wife, Anirul, has been instructed by her Bene Gesserit sisterhood to bear him only daughters. His authority is also challenged by the powerful House Harkonnen, whose illegal stock-piling of the spice melange is of great concern to the Emperor. In order to monopolize the spice, Shaddam and his trusted advisor and friend, Hasimir Fenring, plan to synthesize the substance with the help of Hidar Fen Ajidica, a Tleilaxu Master Researcher. Ajidica sets up laboratories to accomplish this purpose on the newly conquered planet of Ix, formerly the home of House Vernius. By the end of the novel, Ajidica tells Fenring that the manufacture of synthetic spice has been a success, although the validity of his claim is highly dubious.
Leto and his friends, Kailea and Rhombur Vernius, are still struggling to liberate the siblings' former homeworld, but they have made little progress so far.
The Ixian Princess becomes Leto's concubine, though he refuses to marry her for obvious political reasons. Rhombur seeks out a companion from the Bene Gesserit order and is matched with a young woman named Tessia who gives him a new sense of drive and purpose.
Kailea soon gives birth to a son named Victor Atreides.
After the na-Duke's birth, she becomes increasingly dissatisfied with her role as Leto's concubine, wanting the Duke to marry her so that their son can succeed his father someday.
Her so-called lady-in-waiting, Chiara, is actually a Harkonnen agent sent to poison Kailea's mind against Leto.
Jessica is presented to Leto as a gift from the Bene Gesserit, although the Sisterhood has the ulterior motive of using the pair in their breeding program. At first, Leto refuses to have much to do with Jessica and tries to remain faithful to Kailea.
However, as he and Kailea grow farther apart, he begins to seek out Jessica's company and demands answers from her.
Finally, Kailea is driven to make an attempt on Leto's life. Seducing the guard captain Swain Goire, she steals his key to the armory, and causes an explosive device to be planted on Leto's skyclipper. At the last minute, Leto decides to take Victor along with him, and the boy is injured and dies. The Duke is relatively unharmed, but Rhombur Vernius is reduced to little more than a charred lump of flesh.
Fearing that Leto quickly guesses that she is responsible for their son's death and driven by guilt, Kailea kills her lady-in-waiting and then commits suicide by jumping out a window.
The Tleilaxu offer to grow a ghola of Leto's deceased son in exchange for the barely alive body of Rhombur Vernius. Leto ultimately refuses, after much soul-searching, knowing that the Tleilaxu intend only harm towards House Vernius.
Instead, Leto hires Wellington Yueh, an expert in the field of cybernetics, to fashion a cybernetic replacement body for Rhombur.
Leto and Jessica fall deeply in love, leading Jessica to decide to conceive a son for Leto's sake, directly disobeying the Bene Gesserit's order that she have a daughter.
The Baron Harkonnen grows weaker and more corpulent due to the strange disease inflicted upon him by Gaius Helen Mohiam. After killing a slew of doctors who fail to diagnose or alleviate his condition, he hires Dr. Yueh for a massive price. Yueh reveals to the Baron that Mohiam is responsible for his ailment. In response, the Baron attempts to take revenge against the Bene Gesserit, but fails miserably. Meanwhile, the Baron's brother, Abulurd, uncovers the illegal stockpile of spice on Lankiveil.
Rather than turn his brother in to the Emperor, Abulurd, a benevolent ruler and the polar opposite of his brother Vladimir, uses the stockpile to benefit his people. Upon discovery of this, Glossu Rabban, Abulurd's firstborn son, strangles his father to death, an act which earns him the nickname of "Beast." Baron Harkonnen also kidnaps Abulurd's other son, Feyd-Rautha, and tries to raise him as his own.
Young Liet Kynes comes of age and continues the realization of his father's dream of taming the hostile conditions on Arrakis. Also on Arrakis, the Lady Margot Fenring seeks out the Fremen to discover the reason for the disappearance of several other members of the Bene Gesserit order. She finds that the Bene Gesserit have already integrated themselves into Fremen society and implanted the myths of the Missionaria Protectiva into Fremen culture. Gurney Halleck, a farm laborer on Giedi Prime, witnesses the capture of his sister Bheth at the hands of Harkonnen agents. Halleck fights for the release of his sister, Bheth Halleck, and is savagely beaten by the Harkonnen.
After four years of searching for Bheth, Gurney receives a note from her that tells him she is still alive. A Harkonnen census taker tells Gurney that Bheth paid him to smuggle Gurney's family the note.
The man gives Gurney information that leads him to a pleasure house near Mount Ebony. He infiltrates the pleasure house and finds his sister tied to a bed being tortured by two Harkonnen soldiers.
Bheth's larynx has been cut out so that she cannot speak. Gurney is again beaten to a pulp by the soldiers, and when he regains consciousness he is in a Harkonnen slave pit, where he is forced to mine and polish obsidian ore.
The Harkonnen overseers repeatedly try to break Gurney's spirit through a variety of means: beating him, drugging him, and even forcing him to watch while his beloved sister is repeatedly raped and finally murdered.
Gurney finally manages to escape by stowing himself away in a shipment of the ore, which happens to be a gift from Leto Atreides to his concubine Kailea.
Gurney leaves the shipment before it arrives at its final destination and joins the renegade Earl Vernius. After the Earl is killed on Dune, Gurney travels to Caladan to find the Duke's children and swears his loyalty to House Atreides.
Continuity with Frank Herbert's Dune series
The three novels in the Prelude to Dune series provide much information about characters that appear in Frank Herbert's novels. Some of this information seems to more or less agree with Herbert's novels, while other information directly or indirectly contradicts the earlier Dune series.
- Paul Atreides is conceived and Jessica's motives for having a son instead of a daughter are explained in depth.
- The origins of Feyd-Rautha's sadistic personality are revealed.
- Gurney Halleck receives his inkvine scar.
- Dr. Yueh is introduced, and his relationships with Houses Atreides and Harkonnen begin.
- Reverend Mother Ramallo is introduced.
- The origin of "Beast" Rabban's nickname is explained.
- Jessica is tested by Mohiam in a way that is reminiscent of Paul's testing in the first book of the original series. However, while Paul was tested using only sensations of pain, Jessica experiences sensations of pain, pleasure, and eternity successively during her testing.
- Spoilers end here.