In the far future, the known universe is ruled by Padishah Emperor Shaddam IV. The most valuable substance in the empire is the drug melange or "spice", which extends life and expands consciousness. The spice also allows the Spacing Guild to fold space, permitting safe, instantaneous interstellar travel.
The Guild fears a conspiracy that could jeopardize spice production and sends an emissary to demand an explanation from the Emperor, who reveals his scheme to destroy House Atreides. The Emperor fears Duke Leto Atreides' growing popularity—and a secret army he is reportedly amassing—threaten his rule. He plans to cede control of planet Arrakis (also known as Dune), the universe's only source of spice, to House Atreides. Once they are installed there, the Atreides will be ambushed by their longtime archenemies, the Harkonnens, with help from the Emperor's elite Sardaukar troops.
The Guild Navigator commands the Emperor to kill Duke Leto's son, Paul Atreides, because the Guild fears he may somehow threaten spice production. The execution order draws the attention of the Bene Gesserit sisterhood, since Paul is tied to their centuries-long breeding program to produce the Kwisatz Haderach, the universe's superbeing. Before Paul leaves for Arrakis, he is tested by the Bene Gesserit Reverend Mother Mohiam by being forced to place his hand in a box which induces excruciating pain. To Mohiam's surprise and eventual satisfaction, he passes the test.
On the industrial world of Giedi Prime, the sadistic Baron Vladimir Harkonnen tells his nephews Glossu "The Beast" Rabban and Feyd-Rautha about his plan to eliminate House Atreides by manipulating someone in the Duke's orbit to betray him. The Atreides leave their homeworld Caladan for Arrakis, a barren desert planet populated by gigantic sandworms. The native people of Arrakis, the Fremen, prophesy that a messiah will lead them to freedom. Duncan Idaho, one of Leto's loyalists, tells him that he suspects Dune holds vast numbers of Fremen who could prove to be powerful allies.
Before Leto can form an alliance with the Fremen, the Harkonnens launch their attack. The Harkonnens' traitor within House Atreides, Dr. Wellington Yueh (Leto's personal physician), disables critical shields and destroys sonic weapons, leaving the Atreides nearly defenseless. Idaho is killed, Leto is captured, and nearly all of House Atreides is wiped out by the Harkonnens. Baron Harkonnen has Mentat Piter De Vries kill Dr. Yueh with a poisoned blade. Leto dies in a failed attempt to assassinate the Baron Harkonnen using a poison gas tooth implanted by Dr. Yueh. After being wounded by Yueh, Leto let him install the tooth in exchange for sparing the lives of Lady Jessica, his concubine, and Paul.
Paul and Jessica survive the attack and escape into the deep desert, where they are given sanctuary by a sietch of Fremen. Paul assumes the Fremen name Muad'Dib and emerges as the leader for whom the Fremen have been waiting. He teaches them to build and use Weirding Modules—sonic weapons developed by House Atreides—and targets spice mining. Over the next two years, spice production is nearly halted. The Spacing Guild informs the Emperor of the deteriorating situation on Arrakis and demands he rectify it.
Paul falls in love with Chani, a young Fremen warrior. Jessica becomes the Fremen's reverend mother by ingesting the Water of Life, a deadly poison which she renders harmless by using her Bene Gesserit abilities. In a prophetic dream, Paul learns of the plot by the Emperor and the Guild to kill him. He also sees that they fear he will consume the Water of Life. When Paul's dreams suddenly stop, he drinks the Water of Life and has a profound trip in the desert. He gains powerful psychic powers and the ability to control the sandworms, which he realizes are the spice's source.
The Emperor amasses a huge invasion fleet above Arrakis to wipe out the Fremen and regain control of the planet. He has "The Beast" Rabban beheaded and summons Baron Harkonnen to explain why spice mining has stopped. Paul launches a final attack against the Harkonnens and the Emperor's Sardaukar at Arrakeen, the capital city. Riding atop sandworms and brandishing sonic weapons, Paul's Fremen warriors easily defeat the Emperor's legions. Paul's sister Alia mortally wounds Baron Harkonnen, who is sucked through a breached palace wall and into the mouth of a sandworm. Paul confronts the defeated Emperor and fights Feyd-Rautha in a duel to the death. After killing Feyd, Paul demonstrates his newfound powers and fulfills the Fremen prophecy by causing rain to fall on Arrakis. Alia declares him to be the Kwisatz Haderach.
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