Paul is still in the tent, revealing the vast extent of his newfound powers to his mother, Jessica. She thinks Paul is the Kwisatz Haderach, a person with the power to change the universe, but he tells her to forget that idea—he is “something unexpected.” Using his heightened awareness of the future’s possibilities, Paul realizes that he is a product of the Bene Gesserit’s efforts to reinvigorate the human gene pool, but the form that the rejuvenation will take is that of a jihad, or a holy war. The war, led by the remaining Atreides troops and the Fremen, will spread across the universe and disperse the beliefs and laws of the conquerors. The idea of the jihad frightens Paul, and he resolves to try to stop it, if he can.

Paul and Jessica continue to wait for Duncan Idaho’s return. When he does not arrive by nightfall, they decide to move to a new hiding place. As they leave, they see Harkonnen ornithopters blasting the surrounding area, looking for them.

Meanwhile, Thufir Hawat, the Atreides master of assassins, confers with a Fremen elsewhere on the planet. Hawat is amazed that ten legions of Sardaukar and Harkonnen troops were used in the attack—the venture would cost fifty years’ worth of the entire yearly income of Arrakis. The Fremen press Hawat to allow them to take away the bodies of the dead Atreides troops in order to reuse their water. Hawat reluctantly agrees and this secures a sort of bond between the two groups. Hawat is then impressed when several Fremen overpower an ornithopter piloted by Sardaukar and crash it into an enemy troop carrier—it is a feat of combat skill and daring unlike any he has seen. Just as Hawat and the Fremen prepare to move out of the area, the Harkonnen attack and capture Hawat.

Paul and Jessica discover, to their relief, that Duncan and Kynes are piloting the ornithopters surrounding them. Kynes takes them to an ecological testing facility, where they discover that Kynes is also Liet, the godlike, supreme leader of the Fremen. Paul and Kynes negotiate: Paul plans to use the Fremen and their skills to blackmail the emperor into putting Paul and the Atreides on the throne of Arrakis. If the emperor refuses, Paul will show evidence to the Houses of the Landsraad that the emperor sent Sardaukar to destroy the Atreides. If the Landsraad knew that the emperor helped to attack the Atreides, the houses of the universe would unite against the emperor in an immense intergalactic war. Kynes is skeptical, but when Paul pledges his allegiance to Kynes, even at the expense of his own life, Kynes is instantly loyal to Paul in return.

The Sardaukar attack Kynes’s facility, and Kynes helps Jessica and Paul escape; Duncan is killed in the battle. Paul and Jessica take an ornithopter and flee their Harkonnen pursuers. They fly into a sandstorm to cover their tracks, barely keeping the flying machine above the dangerous winds.

The baron’s guard captain tells him that Jessica and Paul must be dead, as no one can stay alive in such a storm. The baron, however, is angry that the captain did not see the dead bodies. The captain also reports that he believes Kynes is a traitor, and the baron orders him to be killed in what looks like an accidental death. The captain also informs the baron that Thufir Hawat has been captured, and the baron decides to convince Hawat to become his personal Mentat. The baron’s nephew Rabban arrives to take control of Arrakis. The baron orders Rabban to squeeze the populace of Arrakis, and to oppress them into submission.

One of the most important motifs in Dune is Paul’s concern that he will be the instigator of a jihad, or holy war, led by the Fremen under his banner. Paul worries that the jihad will spread across the universe as the Fremen and the House of Atreides kill everyone in their path. The reason for this jihad, Paul believes, is that it will reinvigorate the human gene pool, which has been stagnant during the last 10,000 years. Paul wants to resist these possible futures, and he will spend the rest of the novel analyzing his options in every situation, trying to predict their outcome and attempting to take the course that will prevent such a long and bloody war. The jihad is the embodiment of Paul’s sense of “terrible purpose,” a cursed fate that he feels he must resist.

Another important motif in this section is water. On Arrakis, water is much more important than blood because blood cannot exist without water. For example, instead of mourning the loss of lives, Fremen quickly treat the Atreides corpses so they can extract their water; the Fremen ask for the “water bond” with Hawat, which is the equivalent of a blood oath. Now in a situation in which water is a scarce resource, Jessica finds herself thinking more in terms of conserving water. Spitting and crying are considered noble acts because they involve a sacrifice of precious water.

The meeting between Paul and Kynes is a key plot development. Paul wins the loyalty of the Fremen’s secular and religious leader by offering his own unmitigated loyalty. As a result, he recognizes the importance of the Fremen to “desert power,” which is required to maintain control of the planet Arrakis. However, Paul is earnest in his offer of help and in his desire to make Arrakis into an Eden full of plants and animals. Paul’s alliance with the Fremen is partially made out of political necessity—without the Fremen’s help, the Atreides are lost—but also because he believes in and supports the Fremen’s desire to change their world for the better. The meeting scene is also important because it sets up Paul to replace the godlike Kynes as the spiritual and military leader of the Fremen, following the Harkonnens’ murder of Kynes.