A drunk Duncan Idaho, the swordmaster, stumbles into the Atreides castle. Jessica chastises Duncan, who in his drunken state reveals that he suspects that Jessica is a spy for the Harkonnens. Jessica, shocked, calls Hawat to meet with Duncan. She confronts him with his suspicions and tries to convince Hawat that their beliefs are irrational. Jessica explains that it is more logical to believe that the Harkonnens are making Hawat suspicious of her. But Hawat is loyal only to Duke Leto, and he cannot eliminate his suspicion of Jessica. Jessica uses the “Voice” on him, a semi-magical tone of voice that forces Hawat to obey whatever she says. The Voice surprises and disturbs Hawat and makes him think that Jessica is an even more dangerous enemy. When Jessica and Hawat part that night, he is still suspicious.

Late that night, Duke Leto is pondering a strange note he received. He hears an odd sound and investigates, discovering the dead bodies of Tuek and Shadout Mapes. Yueh has shut off the house generators and the shield, leaving the Atreides castle vulnerable to attack. Yueh attacks Leto and informs him that he is placing a false tooth in the duke’s mouth. The tooth will release a great poisonous gas when the duke closes his mouth tightly. He feels badly that he has betrayed the duke, so he tells Duke Leto to bite down on the tooth when he is brought before Baron Harkonnen. This way, Yueh can kill the baron and avenge his wife’s death. However, Yueh still feels some guilt for killing the duke, so he has arranged for Paul and Jessica to escape safely. He takes Leto’s ducal ring to give to Paul as sign of his true intentions for Jessica and Paul to be spare

Sometime shortly thereafter, Jessica and Paul are kidnapped by the Harkonnens. The Harkonnen guards fly them into the desert, presumably to kill the pair. Jessica seduces the two guards and they fight over her until one guard kills the other. Jessica then distracts the remaining guard long enough for Paul to kill him. Paul and Jessica discover a small bundle inside the ship containing food, stillsuits, and other provisions, as well as the ducal ring. As they free themselves, more ornithopters, or small flying ships, appear over the horizon, heading toward them.

Yueh confronts Baron Harkonnen and demands to know what has happened to his wife. As Yueh expected, the baron has killed her, and the baron then orders Piter to kill Yueh as well. The baron’s men bring Duke Leto before the baron, who gloats over his success at defeating the duke. He demands to know where Jessica and Paul have fled, but the duke does not know. The baron threatens to torture Leto. Leto bites down on the poison false tooth, emitting a gas that kills Piter and all the guards, but the baron escapes. One of the Sardaukar, the elite troops of the emperor, demands to see the duke’s body, as the emperor had requested. The emperor’s request causes the baron to lose face in front of his men.

Paul and Jessica are now hiding in a tent from the ornithopters. Fortunately, Duncan Idaho is piloting the ornithopter on instructions from Yueh. Yueh had helped Duncan escape from the baron’s men. Duncan hides Paul and Jessica and then leaves to help the other surviving Atreides men. During this time, Paul changes: his intelligence has become very cold and calculating, but it has also become very powerful. He is able to think ahead of his mother, a Bene Gesserit. Paul reveals to Jessica that the duke always knew she was innocent of treachery. She grieves, but he finds he is unable to grieve with her. As Paul sits, he suddenly has a vision: his intelligence increases, and he has become hyperaware because of the spice he has been eating in his food. He suddenly has a prophetic dream and sees thousands of possible futures. Paul can have these prophesies because of the sudden increased power of his mind and his Mentat-style training. He tells Jessica that she will give birth to a daughter, despite the fact that Jessica has not told anyone she is pregnant. Paul also reveals that both he and Jessica are Harkonnens—the baron was Jessica’s unknown father.

This section describes the key strategies of the Harkonnen trap, showing the baron’s military intelligence. The trap’s complexity suggests that the baron has spent many years devising his plot against the Atreides. The Harkonnen trap includes many different features. First, to bypass the Atreides energy-based defense shields—intended to block lasguns, or laser guns—the Harkonnens use projectile weaponry like bullets, missiles, and artillery fire. Second, the emperor is a party to the baron’s treachery. Therefore, the Sardaukar, the emperor’s ruthless elite troops, will help the baron destroy the Atreides’s troops. The Houses of the Landsraad, the overarching group of families that controls most of the galaxy, would be very upset if they discovered that the emperor had supported the defeat of the Atreides and would likely band together to oust him. To prevent the Landsraad from finding out, the Sardaukar disguise themselves as Harkonnen soldiers. Finally, the baron intends to install one of his own brethren—Rabban, one of his lesser nephews—to rule Arrakis after the Harkonnens take over. The baron wants Rabban to oppress the Arrakeen people and make them hate him, so that when the baron’s beloved nephew Feyd-Rautha arrives to take Rabban’s place, he will be welcomed as a hero. The baron does not just fight against the Atreides, but he also defies his own family members, as well as the Houses of Landsraad, the governing board to which he belongs. His outright abuse of his relationships suggests that he will not be in power for much longer.

Paul, on the other hand, must learn to handle his new superpowers so that he does not abuse them. After the death of Paul’s father, Paul’s character transforms physically, mentally, and emotionally. He kills his first man: the guard on the ornithopter. As he hides in the tent, he also becomes aware of the “terrible purpose” in life that will haunt him for the rest of the novel. Paul must remember his training as a Mentat but also as a Bene Gesserit. Mentats are trained to think only in logical, rational terms; their primary skill is calculating any and every bit of information. Their minds record and analyze everything they see. However, Paul’s mother has also trained him in the more intuitive, spiritual, and mystical powers of the Bene Gesserit. Paul’s success lies in balancing his powers of logic and intuition.

Paul’s ability to handle his new powers is made even more difficult by his use of the magical melange, the spice drug. Melange heightens the user’s awareness of the senses, both rational and spiritual. Paul’s human brain uses only a portion of its potential until he eats the melange spice. He becomes hyperaware of everything around him, and his two schools of training combine to allow him to notice every detail around him, and then plug into a vast mental calculator that computes all the possible outcomes of the future. Some of this computation is mystical as well; there is no logical way that Paul could know his sister would be known as St. Alia of the Knife or that he would meet a girl who would call him Usul. Paul has become a kind of superhuman, capable of combining the skills of a Mentat and a Bene Gesserit. The Fremen will respect Paul’s ability to balance his powers, suggesting that unlike the baron, Paul will rise to become the leader of the universe and will become the Mahdi.