Before we get into the plot, there are a few things to clear up. The universe is made up of many different planets. Kings control each planet. Shaddam IV is the emperor of them all. Duke Leto Atreides, the monarch of Planet Caladan, the homeworld of House Atreides, and Baron Vladimir Harkonnen, king of Planet Giedi Prime, the homeworld of House Harkonnen. The Emperor becomes concerned about these kings because Duke Leto Atreides, with his prosperous planet, has built a far superior army to the Emperor's Salusa Secundus (the Imperial Army Planet), and King Baron Vladimir Harkonen has grown economically more than the Emperor. These kings might succeed him and become emperors someday, so Shaddam IV was determined to destroy them quickly. 

The story begins with a woman recounting some of her people's history on the desert planet Arrakis (a source of spice). The woman, Chani, is a Fremen. She adds that since before she was born, the planet has been governed by the ruthless Harkonnens, who have amassed tremendous wealth by harvesting the psychogenic chemical "melange," also known as spice. (Let me tell you where the spice is harvested and how it is used afterward). The Fremen have attempted to eject the Harkonnens but to no success. The emperor triggers a war between Atreides and Harkonnens. As its initial step, Padishah Emperor Shaddam IV proclaims for the Harkonnens to depart Arrakis. Chani wonders who the future overlords will be.

In the year 10191, on planet Caladan, Paul Atreides shares breakfast with his mother, Lady Jessica, Duke Leto's concubine. Jessica, a quasi-religious Bene Gesserit Order member, has been attempting to teach her son about her group's extraordinary talents. She put Paul to the test by having him try to force her to pass him a drink of water. Paul is just partly successful. Paul learns about the planet Arrakis and its inhabitants, the Fremen, who live in the vast desert with the huge sandworms known as Shai-Hulud. Fremen’s unique blue eyes, known as Ibad's eyes, result from prolonged spice exposure. It is the only source of the psychotropic spice, which increases life expectancy and perception. Spice is required for interstellar travel because it allows Spacing Guild navigators to extend their minds while plotting faster-than-light jumps, "folding" space-time to go instantly and safely from one planet to another.

Leto Atreides, soldier Gurney Halleck, and mentat Thufir Hawat (who excels in logic, computing, and cognitive thinking) welcome an imperial envoy of Emperor Shaddam IV of the House Corrino, who officially awards Arrakis to House Atreides. The emperor is concerned about Leto's growing political influence and popularity in the Landsraad (land council), an assembly of aristocratic households. Leto believes that his nomination to supervise Arrakis is a trap, yet he cannot deny an imperial proposal but accept it. Paul begs his friend, the elite soldier Duncan Idaho, to accompany him when Duncan travels to Arrakis weeks in advance to spy things out. Duncan refuses. Paul admits that he has been having dreams about Arrakis and the Fremen, including one in which Duncan dies in battle. Duncan dismisses this as a dream, informing Paul that "everything important happens when we're awake."

Paul shares his desire to fly to Arrakis early with his father, but Leto refuses, stating that he needs Paul by his side. He describes the political situation: the Emperor has instigated a fight between Houses Atreides and Harkonnen, a war that will weaken both, benefiting the Emperor. Instead, Leto hopes to ally with the Fremen to use their "desert power" to his advantage and deceive the Emperor. Paul questions his ability to succeed his father as a leader. Leto admits to having concerns as a young man and argues that Paul, like himself, will find his way to leadership.

Gurney trains Paul to fight in a better way. During training, they wear protective shields. They activate it once training begins. There is no risk if the shield is blue; if it becomes red, it means the shield has been damaged. Gurney spars with Paul, suggesting that the young ducal heir be careful of the Harkonnens. The House of Harkonnen owned Arrakis for 80 years due to the spice of the fields. Imagine how wealthy they are! Gurney claims that Harkonnens are not people but rather vicious and deadly in warfare. Leto Atreides and the King Baron knew that the Emperor was a dangerous, jealous man who had devised a scheme of devastation. Paul begins to experience dreams about Chani. 

Reverend Mother Gaius Helen Mohiam, Jessica's Bene Gesserit superior and now the Truthsayer of the Emperor, arrives on planet Caladan to test Paul. Before the meeting, he is examined by a Suk doctor (the one who makes no bribe, no warped loyalty, and no other inducement will allow them to bring harm to a human being), Wellington Yueh, who informs Paul that Bene Gesserit has plans to help the greater good. With all due respect to your mother, they also have their agenda. Yueh asks Paul to be cautious. Mohiam puts Paul through the Gom Jabbar test, which involves a poisoned needle and a painful box to assess his character. Mohiam questions Paul, who passed the test, about his dreams and whether they come true on occasion. Mohiam then chastises Jessica for producing a son for Duke Leto instead of the daughters she was supposed to create, as so much potential is wasted in the male. 

She accuses Jessica of believing that her son could be the Kwisatz Haderach, the fulfillment of a Bene Gesserit messianic prophecy. Jessica affirms this notion, and Mohiam states that Paul wields their power and warns her that Paul's abilities are not fully mature and he may die during the upcoming trials. She says that they have done everything they can for her in Arrakis. The route has been laid, and we hope he does not squander it, Mohaim adds. When Mohiam leaves, Paul confronts his mother about what she meant. Jessica reveals that the Bene Gesserit have spent hundreds of years selectively breeding to create an exceptional mind capable of seeing both the past and the future, powerful enough to breach space and time, and one to help them in a better future.

The Atreides arrive in Arrakis. When they depart from the ship, residents begin shouting, “Lisan al Gaib," which Paul does not recognize. When Paul asks his mother, she explains that it is a local prophecy of the Lisan-al-Gaib, the "voice from the outside world," a promised messiah of Arrakis. She says that means that Bene Gesserit has done their work here, as mentioned by Mohiam.

Jessica suggests that Paul could be this figure, but Paul rejects it as a superstition promoted by the Bene Gesserit. Jessica recruits a Fremen servant named Shadout Mapes. Mapes sees Jessica and Paul as a fulfillment of the Lisan-al-Gaib, and she gives Jessica a crysknife crafted from the tooth of Shai-hulud, the massive sandworms that make the Arrakis desert so hazardous. That night, while studying a holographic representation of the sandworms, Fremens’ walking style in the desert to save them from sandworms, and Muad'Dib, the desert mouse, Paul escapes an assassination attempt by a hunter-seeker drone as Mapes enters the room and distracts it. They discover that the Harkonnen agent was cemented into that hole six weeks ago to execute this assassination, and they have manned the hunter-seeker through a water pipe inside the walls. 

Mohiam meets Baron, who has planned to kill all the Atreides, and listens to the Emperor’s message; that is, she tells him that the Emperor will strengthen his army with his Sardaukar army. Mohiam also mentions that “Duke Leto Atreides means nothing to them, but his wife and her son are under our protection and opposed to capture or death. Baron accepts that, and once she departs, he decides to feed them in the desert (sandworms).

Leto assesses his new territory and sees that the Harkonnens have destroyed much of the necessary infrastructure. They decide to take the problem to the imperial transition arbitrator, Liet Kynes, an ecologist who has spent years on Arrakis. Duncan Idaho has returned from several weeks living with the Fremen. He informs the Duke that the Fremen are exceptional combatants who dwell in the community known as "Sietch" in caverns under the desert. Duncan verifies Thufir Hawat's view that there are far more Fremen than previously thought. Duncan says that Arrakis is filled with caverns and millions of Freman. He also mentions that Freman searched for him for days, but they never saw him. So they finally sent a warrior out to kill him and admit that he has never come so close to dying, as Fremen fights like a demon.

Stilgar, the leader of one of these sietchs, has arrived to meet Leto. Stilgar claims that you are outworlders who come to mine spice and leave nothing in exchange. Leto resists, insisting that the Sietchs remain unharmed and that Fremen will not be pursued while the Atreides govern. Paul invites Stilgar to stay, but he departs. Duncan shows the Atreides some Fremen technology, such as para-compass, moisture-saving still suits, and sand compactors that attract sandworms. Duncan also mentions that Fremans are fierce but loyal.

Leto's party meets with Liet Kynes to investigate the spice mining operations. She says they won’t survive two hours without still suits, as it cools the body and recycles the water lost to sweat. She adds that the suits gain power through their body movement, and they can drink the recycled water that will be stored inside the suit's mask.  She examines their still suits and discovers that Paul has intuitively fitted his still suit in the Fremen style. In her home language, she says, "He will know your ways as if he were born with them." The group travels out to inspect a spice mining operation. The "Sandcrawler" mining vehicle has attracted a worm enticed by the crawler's rhythmic vibrations as it gathers the spice. When a flying carry-all fails to remove the mining truck because those kinds of damaged carry-alls and trucks are what Harkonnens had left intentionally. Duke Leto deploys a small squadron of ornithopters nearby to rescue the workers. 

When Paul steps out to guide the miners inside, he is hit with a tremendous dosage of spice and experiences a series of visions, including one of himself with Chani. He is almost pulled down into the sand by the crawler when Gurney grabs him and drags him onboard his father's ornithopter. The two watch as the worm's massive, toothed maw opens, swallowing the sandcrawler completely. Later, Paul is evaluated by Dr. Yueh, who advises Paul and his mother that the spice is psychotropic but will not harm him. Still, Paul mentions that it was not an allergic reaction but a vision he had about a girl (Chani) killing him with the knife. Paul says that he also knows that his mom is pregnant now.

In Salusa Secundus, the Emperor's elite military force, Sardaukar, awaits the Emperor's command to beat the Imperium's greatest legions, Aterides, whom Gurney Halleck and Duncan Idaho have trained. Duke Leto wakes up at night with the feeling that something is awry. He contacts security but receives no response. He discovers Mapes stabbed to death and is hit with a paralytic dart that burrows through his body shield and into his back, rendering him useless. Yueh reveals himself as a traitor. He has dropped the shields and disrupted Atreides' communications. The Atreides troops caught off guard and outnumbered by Harkonnen and Sardukar, are rapidly overwhelmed. Yueh informs Leto that the Harkonnens secured his compliance by holding his wife captive. He takes Leto’s ring for Paul and replaces one of Duke Leto's teeth with a poison capsule, hoping the Duke will use it to kill the Baron.

Gurney is awakened and leads the counterattack as the Harkonnen forces, assisted by imperial Sardukar warriors, launch their assault. Duncan kills numerous Sardukar, takes an ornithopter, and attempts to rescue Paul and Jessica, but discovers they have already vanished. Baron Vladimir Harkonnen had assured Mohiam and the Bene Gesserit that he would not hurt Paul or Jessica, so he ordered some of his soldiers to take them to the desert, where they would die from exposure. Paul, who is not quite confident in his Bene Gesserit powers, can use the voice to direct one of the men to remove his mother's gag. Jessica instantly orders one of the soldiers to kill his friend. When she is fully liberated, she murders two of them directly. Their ornithopter is remotely shut down and lands. Paul and Jessica observe the wreckage of Arrakeen from a distance.

Baron has Leto under his custody. Paul finds a letter in a bag from Yueh stating, “If anyone makes it out of Arrakeen alive there’s an Atreides beacon in the Fremkit. God willing they’d be able to find you.” Yueh meets with Baron Harkonnen and demands that he keep his part of the arrangement. The Baron assures Yueh that he will be reunited with his wife before slitting his throat. On the other side, Paul finds a thumper and his father’s ring. The Baron then gloats over a paralyzed Leto, who bites down on his fake tooth and expels the poison, killing everyone in the room except the Baron, who is severely damaged after activating his body shield and floating to the roof. Medical technicians are nursing the Baron back to health.

Paul, riding out a storm in a survival tent, is still experiencing images from his spice exposure. They are the first of Chani. However, they quickly transform into images of brutal battles and religious zealots working under the Atreides banner and in Duke Leto's name, spreading across the galaxy "like an unquenchable fire." Images of fanatical armies worshiping at the shine of Leto's skull, everyone crowing his name and fighting in his honor. Paul is appalled by what he sees and blames both his mother and the Bene Gesserit but is eventually consoled by his mother.

Duncan Idaho, who had escaped the slaughter, rescues Paul and Jessica. Duncan transports them to Kynes, who has set up in an abandoned terraforming station populated by Fremen. The Sardukar tracks them down and attacks, with the Fremen killing many. Duncan gives his life in a last stand to allow Paul, Jessica, and Kynes to escape. Paul and Jessica flee via ornithopter. Kynes sets up a thumper to summon a sandworm and ride it away, but the Sardukar fatally wounds her. Before they can execute the final blow, a sandworm appears, and Kynes draws it to her by hammering a piece of drum. The worm swallows them all.

While piloting the ornithopter through a violent sandstorm, Paul has a vision of a Freman giving him advice, reminding him that survival in the desert is a process and that he must adapt to the environment. Paul retracts the 'thopter's wings, allowing the storm's vortex to carry it deeper into the desert. Meanwhile, Rabban informs Baron that their teams had pursued Paul into the Coriolis storm; nothing survives that storm, and they would undoubtedly die. Eventually, Paul and Jessica survive the storm, but the ornithopter is destroyed, forcing them to walk through the desert, heading to find the Freman to join them. In his vision, he sees Chani and a man who invites him to join him in the desert to learn more about it. Paul teaches Jessica the sandwalk as they prepare to enter worm territory. They will die if they walk like humans. Fremen keeps an eye on them as they go.

Jessica and Paul make their way to where they think the Fremen's sietch is. Their motions attract a sandworm, and they flee for some nearby rocks. The sandworm pauses for a few seconds as if peering at Paul, before being drawn away by a thumper. A group of Fremen apprehends them. Stilgar is among them and recognizes Paul, stating that they cannot touch him. Another Freman, Jamis, was the one who distracted Worm with a thumper. Jamis rejects Stilgar's belief and intends to murder Paul and Jessica and steal their bodies for water. 

Jessica requests assistance returning to Caladan, claiming that they will be highly compensated, but Stilgar dismisses any payment as worthless. Stilgar agrees to let Paul, who is still young, join their sietch, but Jessica, whom he believes is too old to learn to battle, must be left behind. Jessica and Paul use their Bene Gesserit expertise to disarm most Fremen and keep Stilgar at knifepoint. Stilgar, realizing Jessica is a Bene Gesserit, relents and agrees to take both of them to the Sietch Tabr to decide the fate of the strangers. Paul recognizes Chani, the girl he saw in his dream. Jamis disagrees and claims that the strongest leads. Jamis says, now that she has bested you, I invoke the Amtal (testing to destruction). And he challenges Jessica to a duel. Stilgar claims that he cannot challenge a Sayyadine (Friend of God). Paul also recognizes Jamis as the man in his visions.

So Paul agrees to serve as his mother's champion. Chani, who is among the party, feels sorry for Paul, who she believes will die at Jamis' hands, and gives him her crysknife to die in honor. It’s a dagger crafted from a sandworm, Shai-Hulud’s teeth, a scene from one of Paul's dreams. In the duel, Paul outclasses Jamis by repeatedly placing a knife in his throat and demanding that he surrender. Stilgar warns him that Fremen duels are to the death, but Jessica claims Paul has never murdered anybody before. Paul reluctantly murders Jamis. Satisfied, the Fremen return Paul and Jessica to their sietch.

Paul and Jessica witness a Fremen riding a live worm. As they start their journey into the desert, Chani warns Paul, “This is only the beginning.”