It is approximately the year 20,000 CE — or thereabouts; it's been 10,191 years since the Spacing Guild Hit So Hard, the Calendar Felt It. Humanity has colonized the stars, and much culture has blended; there is a faith called "Zensunni", for instance, blending tenets of Zen
Buddhism and Sunni Islam. Humankind is heavily dependent on the Fantastic Drug "melange", or simply "spice": not only is it nigh-universally-useful, it's specifically what allows Faster-Than-Light Travel. Spice can only be found only on the Thirsty Desert planet Arrakis, known colloquially as Dune. There are a number of galaxy-spanning organizations, like the Spacing Guild, the Landsraad and the Mentat human computers; one such, the "Bene Gesserit", an all-female Covert Group with Mundane Front, have spent centuries quietly steering the species toward what they consider the best path. One of their more recent moves, spearheaded by the current Reverend Mother Gaius Helen Mohiam, was to send her student Jessica to marry Duke Leto Atreides, ruler of the planet Caladan. House Atreides and House Harkonnen have been Feuding Families for centuries; and Jessica, who like every Bene Gesserit is a Femme Fatale, was to produce a daughter who could end the feud via Altar Diplomacy. But Jessica, a Hooker with a Heart of Gold, complied with her husband's wishes to give him a son: 15-year-old Paul Atreides, The Protagonist.
Each chapter is prefaced by an excerpt from Fictional Documents concerning Paul, all of them written by one Princess Irulan.
Book 1: Dune
The book opens as Mohiam tries to salvage things by giving Paul a test, requiring him to keep his hand inside a box that causes horrific pain, under threat of being stabbed with a lethal poisoned needle called a gom jabbar. Paul summons the willpower to endure the pain until the test ends, and the pleased Mohiam declares him a human rather than an animal, able to use reason to overcome his base instincts. Lady Jessica admits that she has been training Paul in Bene Gesserit secrets, things normally reserved for girl-children, and Mohiam both censures her and admits she would have done the same. The Reverend Mother also asks Paul about his habit of Dreaming of Things to Come, which are implied to be a part of his unusual destiny.
Baron Vladimir Harkonnen sets in motion a complex plan to wipe out the Atreides, manipulating Emperor Shaddam into reassigning Leto to oversee the spice mining on Arrakis, after which he will destroy the mines and make a fortune with his own stockpile of spice. Leto sees right through the plot, but goes along on "Trap Is the Only Option" grounds. He and his closest lieutenants — Thufir Hawat, Mentat and The Spymaster; Warrior Poet Gurney Halleck; Master Swordsman Duncan Idaho — plan to use Arrakis, a Death World in the best of circumstances, as a place to conduct Training from Hell; particularly, they hope to ally with the planet's native Proud Warrior Race, the Fremen, and find for themselves a Badass Army. This is their primary defense against the Emperor, whose Elite Army, the Sardaukar, are recruited from a similar Death World called Salusa Secundus. The Reverend Mother believes Leto is doomed to failure in this endeavor.
Shortly after their arrival, Paul narrowly survives an assassination attempt with a remote probe, and Jessica receives a letter from a fellow Bene Gesserit, warning her that there is a traitor in the household. In better news, Duncan Idaho gains the support of Stilgar, the local Fremen leader.
In a subplot that has been universally discarded from film adaptations, the Baron arranges for Thufir Hawat to find a letter implicating Jessica in a plot to betray Leto. Leto isn't fooled by this clumsy frame, but decides to let the rest of the staff believe it while confiding only in Paul.
The Imperial Planetologist Kynes, who also serves as the Emperor's proxy during the handoff of Arrakis, shares Leto's dream of terraforming Arrakis, and takes Leto and Paul to see a spice mine. The mine is attacked by a gigantic Sand Worm, and when the carryall that typically rescues miners fails to appear, Leto immediately decides to sacrifice the spice in favor of saving the crew. Leto does this despite knowing full well that Harkonnen saboteurs are probably behind the missing carryall, and that the dent on the galaxy's bottom line will be held against him. Kynes, who had been bribed by the Baron to sabotage Leto, is so impressed by the Duke's "The Men First" attitude that he performs a Heel–Face Turn on the spot.
While the Baron's plan to discredit Jessica fails, it does have the effect (intentional or otherwise) of causing Thufir, the most Properly Paranoid of the Atreides retainers, to focus his suspicions on her. This lets the real traitor through: House Atreides' staff physician Wellington Yueh, who despite nominally being Beneath Suspicion (due to the brainwashing inherent in his training as a Suk School doctor) has been blackmailed through the simple expedient of Baron Harkonnen having his wife.note Yueh shuts off the palace defenses so the Harkonnen forces can attack; they are aided by several legions of Imperial Sardaukar wearing Harkonnen uniforms to give the Emperor Plausible Deniability. As they attempt to knit up the unraveling Atreides structure, Thufir and Gurney note that the Fremen are better fighters than the Sardaukar, and that their plan might've succeeded with only a few more months; but now it's too late. The Atreides are routed and the Duke captured. But Yueh, like most victims of the "I Have Your Wife" trope, is a Regretful Traitor: he hides a Cyanide Pill in Leto's mouth which will expel poison gas, sufficient for him to pull a "Taking You with Me" on the Baron, and arranges for Jessica and Paul to escape into the desert. The Baron has Yueh Rewarded as a Traitor Deserves, and even more unfortunately escapes the gas attack which only kills his spymaster Piter de Vries.
In the desert, Paul discovers that his dreams of the future have been amplified by the spice that saturates the Arrakeen diet, and not only consoles Jessica that Leto knew she was faithful, but reveals he knows she is pregnant with a daughter, and also that she is the illegitimate daughter of the Baron. Jessica realizes that Paul has become the thing the Bene Gesserit have been trying to create with their breeding program: the Kwisatz Haderach, literally "The Shortening of the Way" in Hebrew. While the original term refers to teleportation, what Paul is able to do is see the future, and therefore guide humanity to a better tomorrow. This was the other reason Jessica was instructed to bear a daughter: that child, Pauline, was to mate with a Harkonnen and produce the Kwisatz Haderach; however, this has proved to be unnecessary, as Paul is here, now. Paul, however, is horrified at what the future seems to hold for him.
- He had seen two main branchings along the way ahead—in one he confronted an evil old Baron and said, "Hello, Grandfather." The thought of that path and what lay along it sickened him.
The other path held long patches of grey obscurity except for peaks of violence. He had seen a warrior religion there, a fire spreading across the universe with the Atreides green and black banner waving at he head of fanatic legions drunk on spice liquor. Gurney Halleck and a few others of his father's men—a pitiful few—were among them, all marked by the hawk symbol from the shrine of his father's skull.
"I can't go that way," he muttered. "That's what the old witches of your schools really want."
—Frank Herbert, Dune, pg.195 (40th Anniversary edition)
Book 2: Muad'Dib
Kynes and Duncan rescue Duke Paul and Jessica, and takes them to one of his facilities where he reveals he's actually a leader amongst the Fremen, the quasi-divine Liet, having Gone Native. The Harkonnens soon attack, and Duncan sacrifices himself so the others can escape. Back at the palace, the Baron learns that Hawat has been captured and decides to try to convince him to switch sides. He's also forced to change his plan for Arrakis, which would have involved Piter ruling as a monstrous tyrant until the Baron's nephew Feyd-Rautha overthrew him, gaining the support of the people. Instead, he substitutes his other nephew Glossu Rabban, who has already served a tenure as planetary governor and was already a monstrous tyrant during that time.
As Paul and Jessica suffer traveling through the harsh desert for several days, the Atreides warmaster Gurney Halleck manages to escape the Harkonnens and falls in with a group of Fremen smugglers, and Kynes is dumped into the raw desert to die when his betrayal of the Harkonnens is discovered. Paul and Jessica are attacked by a sandworm, but it's drawn away by Fremen led by Stilgar. He's skeptical about helping them, but Jessica takes advantage of the fact that the Bene Gesserit Mage Species are Crazy-Prepared and have sown legends about themselves amongst the Fremen. She also, like every Bene Gesserit, Minored in Ass-Kicking, and is so adept at Waif-Fu that she is able to best Stilgar himself. Asskicking Leads to Leadership amongst the Fremen — especially when you consider that, by doing this, Jessica may have proved herself to be the greatest fighter in the known universe — and they eagerly accept her offer of teaching them the "weirding way" in exchange for protecting the Atreides refugees.
Of course, no culture is a Planet of Hats, and some of the Fremen resist. One of them in particular, Jamis, invokes a Duel to the Death with Paul, determined to prove that the outsider is too soft to live amongst the Fremen — or to die trying. This is a watershed moment for Paul, not only because it alerts him to the many subtle ways in which his fighting style has been adapted to the Deflector Shields that are used everywhere else, not only because he's already gotten dependent on seeing the future, but because he has never before killed a man. Nonetheless, he wins without taking so much as a scratch, and is welcomed into the sietch. At Jamis' funeral, he is called upon to speak tribute to the man, and ends up shedding tears over him — a sacred gift to a desert-dwelling people.
On the Harkonnen homeworld of Geidi Prime, Hawat has agreed to work for House Harkonnen (since this will allow him to position himself better for revenge). He agrees to help Feyd-Rautha cheat in a gladiator combat to impress the visiting Count and Lady Fenring, another Bene Gesserit who has plans to become pregnant by Feyd-Rautha to set their plans back on track. (She's also the lady who sent Jessica the warning letter back in the first volume of the book.)
Stilgar advises Jessica that their own Reverend Mother will die soon and she should take the position to give herself a place in their society. Paul is recognized as a figure from the Bene Gesserit legends — the "Lisan al-Gaib," the Voice from the Outer World — who will lead them to prosperity, and is given the secret name Usul as well as the common name Muad'Dib, after the kangaroo mouse, to cement his place among them. He also grows close with Kynes' daughter Chani after recognizing her from dreams where she called him Usul.
Jessica goes through the ritual to become the new Reverend Mother, which involves converting a poison, "The Water of Life," to be safe to drink, and allowing the memories of all previous Reverend Mothers inside her. The woman she is replacing is horrified to realize she's pregnant: her daughter will also absorb the memories. (This becomes important later.) Afterward, Jessica upends tradition by inviting all the Fremen to partake in the liquid and gain its powers. This completes Paul's transformation into a Seer of the future, and he and Chani, propelled by the knowledge that they will fall in love, begin to fall in love.
Book 3: The Prophet
Two years later, Paul is a beloved figure among the Fremen, though they're disturbed by his sister Alia who already acts like an adult due to the ceremony. Paul also has a son with Chani, Leto II, and undergoes an important rite of passage, calling and riding a sandworm. Hawat, meanwhile, has busied himself playing the Baron's own game by creating dissent between him and Feyd-Rautha. He's also confirmed that House Atreides' speculation on the Sardaukar — and the Fremen suitability as a counter-force due to their Training from Hell — were accurate, and suggests House Harkonnen take up a similar program to further cause resentment on Arrakis. The first step is cutting off support to Rabban whilst simultaneously demanding he crack down on the planet.
Many Fremen have been urging Paul to challenge Stilgar for leadership, but he refuses and insists Stilgar remain their secular leader while he takes his rightful place as Duke, with Stilgar (consensually) swearing fealty to him. The Fremen attack the smugglers Halleck joined, leading to a reunion, and Paul is able to convince Halleck his mother was innocent. Some of the smugglers turn out to be Sardaukar, and after the Fremen defeat them, Paul lets some escape to tell the Emperor about the power he wields. They also learn about Rabban's abandonment, and decide the time is ripe for an attack. But first he takes The Water of Life, which puts him in a coma for weeks until Jessica is desperate enough to summon Chani. Paul wakes up upon her arrival, and reveals he had a vision about a place in the mind of all Bene Gesserit where they dare not look — the male half of their Genetic Memory, which only he can see. He is the thing the Bene Gesserit have been trying to create this whole time: a Reverend Father. He has finally, irrevocably, become the Kwisatz Haderach.
The Baron and The Emperor arrive at Arrakis, and attack Paul's home while he is away preparing the assault, killing Leto II and capturing Alia. Paul leads the counterattack under cover of a massive sandstorm, and the people of Arrakis are driven to rise up alongside the Fremen, killing Rabban. Mohiam is also present as the Emperor's advisor and is terrified of Alia, calling her an abomination. They're interrupted as the Fremen break through, and in the confusion Alia kills the Baron. The Fremen disable all the Emperor's ships, and Paul makes his camp in the ducal manor his father once inhabited before sending the Emperor terms for surrender. The Emperor tries to coerce Hawat into a Suicide Attack on Paul, but Thufir refuses, preferring to turn the weapon on himself. Paul then threatens to destroy all the spice, causing the various Guilds to turn on the Emperor and leave him powerless. The Emperor tries to persuade Count Fenring to intervene, but he also refuses, and is even revealed to have almost been the Kwisatz Haderach himself. Paul also turns on Mohiam, declaring that he may be the Kwisatz Haderach but he still refuses to follow her plan. Feyd-Rautha makes a last-ditch attempt to challenge Paul to single combat, and cheats as usual, but Paul still defeats him. Finally, he forces the Emperor to abdicate and to give away his daughter Princess Irulan — yes, the historian who provided all the Fictional Documents — in marriage, giving Paul full legitimate control of all humanity (even as Chani, officially his concubine, remains his One True Love), determined to create a prosperous new age.
That said, the novel also ends on an ominous note. Ever since discovering he was the Kwisatz Haderach, Paul has seen that his actions could lead to a holy war in his name which will consume the Imperium in violence and bloodshed. He has been doing his best to make choices that steer the galaxy away from this outcome. As he takes the throne, Paul discovered that Failure Is the Only Option; the choices themselves have cemented himself as a Famed In-Story Living Legend, and his followers — or, rather, worshippers — got locked into the Holy War somewhere along the way. Paul may be The Protagonist, but the Aesop of the story is to Beware the Superman, and his story has been that of Protagonist Journey to Villain. House Atreides triumphs... But what's going to happen to the galaxy after the final page is going to make every preceding war look like a vacation.
