Dune: Part Two runs from Paul's first weeks among the Fremen to a war he cannot take back. It opens with the survivors of the Atreides collapse, Paul and Jessica, entering the tribe's world, where Paul has to prove himself. He does so by defeating Jamis in a duel, and Jessica drinks the Water of Life and inherits the memories of earlier Reverend Mothers.
Paul then learns the desert, rides a sandworm for the first time, and joins Chani in raids on the spice harvesters. Chani does not share the belief many Fremen hold about him, because she reads the prophecy as a Bene Gesserit invention. Back at the Harkonnen end of the story, the Baron sets aside Rabban and puts Feyd-Rautha in charge, and the attacks on the Fremen grow harsher. Paul keeps seeing a galactic holy war in his visions, and that fear makes him hold back from leadership.
A Harkonnen assault changes his mind. He travels south, drinks the Water of Life and sinks into a coma, and Jessica brings him back. He comes out knowing the full truth of the Bene Gesserit breeding plan that produced him, and he claims the title of Lisan al Gaib, which gathers the Fremen behind him.
Paul's threat to the spice fields draws Emperor Shaddam and his forces to Arrakis. The Fremen answer with atomic weapons and sandworms and break the Harkonnen and imperial troops. Paul kills the Baron, Gurney kills Rabban, and Paul claims the throne. The Emperor puts Feyd-Rautha forward as his champion, and Paul kills him in a knife duel.
Irulan agrees to marry Paul so that her father is spared. The other Great Houses still reject his claim, so Paul orders an attack on their fleet. Chani is horrified by the political marriage and the war ahead, refuses to bow to him, and leaves alone on a sandworm.