Paul Atreides, the son of Duke Leto and his concubine Jessica, passes the test given by a Reverand Mother (thanks to Jessica's Bene Gesserit training) and is thus declared human. The Atreides family has been given rule over the planet Arrakis, or Dune, as a political move by the Harkonnens, their arch rivals. Soon after arriving, the Harkonnens leverage a traitor (Dr. Yueh) to kill the Duke and allow the Emperor's soldiers (Sardaukars) into the household. Paul and his mother (who is pregnant with a girl) flee into the deep desert to escape the slaughter. Duncan Idaho gives his life to buy time for Jessica and Paul to escape. Gurney Halleck and Thufir Hawat survive, with Gurney joining a band of smugglers and Hawat being forced into servitude as Baron Harkonnen's mentat. Liet Kynes, the leader of the Fremen tells Paul and Jessica to find the Fremen, but he is also captured and killed in the process.

The deep desert of Dune is occupied by huge sand worms that devour anything they find on the sand. However, as Paul and Jessica soon learn, it is possible to avoid a worm by moving through the desert making only the natural sounds of the desert. As they escape a worm, they stumble upon a band of Fremen, led by Stilgar (Kynes's brother). Paul disarms a Fremen, and Jessica overpowers Stilgar, buying enough time to explain who they are. The Fremen begin to think that Paul may be the Lisan-al-Gaib (a prophet out of legend). Jamis, the man Paul disarmed, challenges him to single combat, and Paul kills him, inheriting his water and his family (a wife and two children). Paul becomes a Fremen and is now known as Usul or Muad'Dib.

Paul and Jessica arrive at Tabr Sietch where Paul eats something filled with the spice (mélange). It causes him to enter a state of prescience, and he learns that his status as a prophet among the Fremen could lead to a Jihad across the universe. He also realizes that Chani, Kynes's daughter, is destined to be his lover and the mother of his children. Jessica is given the Water of Life (water that has been tainted by a Maker (worm) that is drowned). It is poison, but she is able to convert it so that the entire sietch can consume it safely. By doing so she establishes herself as a Reverand Mother, and obtains the memories of all the Reverand Mothers before her. During the process, however, her unborn daughter also obtains these same memories and powers. While in the sietch Paul and Jessica also learn that the Fremen have been working in secret to convert the desert of Arrakis to a place full of water and life. They have millions of liters of water stored until there is enough to make the conversion possible.

Years pass and Paul has established himself as a leader among the Fremen, and he and Chani have had a baby boy. Paul is tested again, this time with the task of riding a wild Maker. He passes the test, but soon after his men come across a "thopter. They ambush it, only to discover that Gurney Halleck is among them. He joins Paul. These events spur Paul to stake his claim as Duke and rightful ruler of Arrakis. They soon plan an attack against the Harkonnens. Sensing the impending conflict, the Emporer, all the major Houses, and the Harkonnens travel to Arrakis to lay claim to what spoils of war they can. Paul and the Fremen, however, attack under the cover of a storm, completely decimating the Emperor's Sardaukar forces. Unfortunately, Alia (Paul's younger sister) is captured and his son Leto is killed.

The Emperor brings Alia in for questioning, but she kills the Baron (her grandfather through Jessica) and escapes just as the battle begins. The Emperor and his entourage are brought before Paul. The Baron's nephew challenges Paul to single combat. Paul accepts and kills him, despite the poison on his opponent's blade. Thufir Hawat is also there, but he kills himself rather than betray the Atreides family (as the Emperor commanded him to). Finally, Paul outmaneuvers the Emperor, who agrees to let Paul marry his daughter (Irulan) in order to let Paul become the Emperor. The book ends with Jessica comforting Chani with the knowledge that, while Paul may be married to Irulan in name, history will remember her as Paul's wife.