At the end of Dune Messiah, Paul Atreides walks into the desert, a blind man, leaving his twin children Leto and Ghanima in the care of the Fremen, while his sister Alia rules the universe as regent. Awoken in the womb by the spice, the children are the heirs to Paul's prescient vision of the fate of the universe, a role that Alia desperately craves. House Corrino schemes to return to the throne, while the Bene Gesserit make common cause with the Tleilaxu and Spacing Guild to gain control of the spice and the children of Paul Atreides.
Herbert chose in the books that followed to undermine Paul’s triumph with a string of failures and philosophical paradoxes; Dune was a heroic melody, and Dune Messiah was its inversion. When the second novel, Dune Messiah, opens, Muad’Dib’s religion has sent his fanatical soldiers on an interstellar religious rampage, leaving billions dead. His vision of peace is being corrupted by dogmatic religious bureaucrats, and his once-noble desert tribes, the Fremen, are fat and wealthy on the spoils of war and the de-desertification of Dune.
When Children of Dune picks up the tale, Muad’Dib has become an old man damaged by forced overdoses of spice essence and dependent on an assistant; he is rousing the populace against the priestly apparatus and its ruler — his sister Alia, who has since lost the battle with the memory personalities she contains, and is possessed by the persona of her grandfather and Atreides enemy, Baron Harkonnen.
Despite numerous enemies, Muad'Dib's children Leto and Ghanima survive concerted attempts to eliminate them. Leto undertakes a transformation by allowing sandtrout to bond to the surface of his body, making him immensely strong and fast and beginning his transformation into a human-sandworm hybrid. The subsequent deaths of Paul and Alia lead to the virtually immortal Leto grasping control of the Known Universe.
Over and over, Herbert shows how his characters' triumphs contain the seeds of their own destruction, and how their personalities and ideals keep them on the track of destruction, even if prescient vision proves to them how they are doomed. Frank Herbert said later in life that he conceived all three of the first Dune books as a single story from the start, and that he simply produced that one complete tale in three separate volumes. None of the sequels ever matched the original in sales or influence, and none tackled quite so epic global political events. Instead, Herbert used the compelling world he had created as the backdrop for increasingly cryptic meditations on ecology, politics, and power.