In the far future, the known universe is ruled by Padishah Emperor Shaddam Corrino IV; the most precious substance in his sprawling feudal galactic empire is the spice melange, which extends life, expands consciousness, and is vital to space travel. The powerful Spacing Guild and its prescient Navigators use the spice to "fold space" and safely guide interstellar ships to any part of the universe instantaneously.
Sensing a potential threat to spice production, the Guild sends a Navigator to demand an explanation from the Emperor, who confidentially shares his plans to destroy House Atreides. The popularity of Duke Leto Atreides has grown, and he is suspected to be amassing a secret army using sound weapons called Weirding Modules, making him a threat to the Emperor. Shaddam's plan is to give the Atreides control of the planet Arrakis, the only source of spice in the universe, and to have them ambushed there by their longtime enemies, the Harkonnens. Informed of this plot, the Navigator commands the Emperor to kill the Duke's son, Paul Atreides, a young man who dreams prophetic visions of his purpose. The cryptic assassination order draws the attention of the Bene Gesserit sisterhood, as Paul is tied to their centuries-long breeding program which seeks to produce the superhuman Kwisatz Haderach. Paul is tested by the Bene Gesserit Reverend Mother Gaius Helen Mohiam. With a deadly gom jabbar at his throat, Paul is forced to place his hand in a box which subjects him to excruciating and increasing pain; he passes to Mohiam's satisfaction, withstanding more pain than anyone has before him. Meanwhile, on the industrial world of Giedi Prime, the sadistic Baron Vladimir Harkonnen tells his nephews Glossu Rabban and Feyd-Rautha about his plan to eliminate the Atreides by manipulating someone very close to the Duke into betraying him. The Atreides leave their watery world of Caladan for Arrakis, a barren desert planet plagued by gigantic sandworms and populated by the Fremen, mysterious people who have long held a prophecy that a messiah would come to lead them to true freedom. Upon arrival on Arrakis, Leto is informed by one of his right-hand men, Duncan Idaho, that the Fremen have been largely underestimated, as they exist in vast numbers on Arrakis and could prove to be powerful allies. Leto gains the trust of the people of Arrakis, proving to be a charismatic and just leader. But before the Duke can establish an alliance with the Fremen, the Harkonnens launch their attack.
While the Atreides had anticipated a trap, they are unable to withstand the devastating Harkonnen sneak attack, supported by the Emperor's elite troops, the Sardaukar, and aided by a traitor within House Atreides itself, Dr. Wellington Yueh. Captured, Leto dies in a failed attempt to assassinate the Baron Harkonnen using a poison gas capsule planted in his tooth by Dr. Yueh. Leto's concubine Jessica and his son Paul escape into the deep desert, and with Jessica's Bene Gesserit abilities and Paul's developing skills, they manage to join a band of native Fremen. Paul emerges as Muad'Dib, the religious and political leader the Fremen have been waiting for. Paul teaches the Fremen to use the Weirding Modules and begins targeting mining production of spice. In the span of two years, spice production is effectively halted. The Emperor is warned by the Spacing Guild of the situation on Arrakis, and the Guild fears that Paul will consume a substance known as the Water of Life. These fears are revealed to Paul in a prophetic dream; he drinks the Water of Life and enters a coma that disturbs all Bene Gesserits in the universe. Awaking, Paul is transformed and gains control of the sandworms of Arrakis. He has also discovered the secret to controlling spice production; water kept in huge caches by the Fremen can be used to destroy the spice. Paul tells his army of Fremen "he who can destroy a thing controls it." Paul has also seen into space and the future; the Emperor is amassing a huge invasionary fleet above Arrakis to regain control of the planet and the spice.
Upon the Emperor's arrival at Arrakis, Paul launches a final attack against both the Harkonnens and the Emperor at the capital city of Arrakeen. His Fremen warriors, armed with Weirding Modules and riding sandworms, defeat the Emperor's legions of Sardaukar while Paul's sister Alia kills the Baron Harkonnen. Paul faces the defeated Emperor, and avenges his family in a duel to the death with Feyd-Rautha. After defeating Feyd, Paul commands rain to fall on Arrakis. Alia reveals to everyone that Paul is indeed the Kwisatz Haderach.