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This episode starts 12 years after the first Dune miniseries. Duke Paul Atreides has become emperor. During an attack he is blinded but utilizes his "visions of the future" to see. Chani his concubine has given him twins - Leto II and Ghanima. When his children are attacked, Paul uses Leto's eyes to see and avert the danger, but in the process loses his psychic vision and becomes completely blind. In accordance with Fremen custom, he walks into the desert and leaves his children in the care of his sister, Alia.

As conspiracies to gain political power abound, Paul's power base is eroded from within and his highly ambitious sister, Alia is gaining a political foothold. Born aware of her ancestral memories, Alia is considered an abomination by the Bene Gesserit. The Lady Jessica, her mother returns to Dune (Arrakis) to visit her grandchildren Leto II and Ghanima. When one particular ancestor begins to possess Alia, Lady Jessica has to take refuge. Leto II and Ghanima devise a plan toward salvation.

As Alia becomes totally possessed she also has to deal with rebel Fremen. Ghanima, who survived an attack on her by House Corrino, is now engaged to Farad'n Corrino. Unexpectedly, Leto II returns from the desert being believed dead. While in the desert his body has absorbed some sandtrout, slowly mutating him into a sandworm. Alia resists possession by the baron while Irulan declines Jessica's offer to return with her to Caladan.