The Bene Gesserit find themselves the target of the Honored Matres, whose conquest of the Old Empire is almost complete. The Matres are seeking to assimilate the technology and superhuman skills of the Bene Gesserit, and exterminate the Sisterhood itself. Now in command of the Bene Gesserit, Mother Superior Darwi Odrade continues to develop her drastic, secret plan to overcome the Honored Matres. The Bene Gesserit are also terraforming the planet Chapterhouse to accommodate the all-important sandworms, as the planet Dune had been destroyed by the Matres.

Sheeana, in charge of the project, expects sandworms to appear soon. The Honored Matres have also destroyed the entire Bene Tleilax civilization, with Tleilaxu Master Scytale the only one of his kind left alive. In Bene Gesserit captivity, Scytale possesses the Tleilaxu secret of ghola production, which he has reluctantly traded for the Sisterhood's protection. The first ghola produced is that of their recently deceased military genius, Miles Teg. The Bene Gesserit have two other prisoners on Chapterhouse: the latest Duncan Idaho ghola, and former Honored Matre Murbella, whom they have accepted as a novice despite their suspicion that she intends to escape back to the Honored Matres.

Lampadas, a center for Bene Gesserit education, has been destroyed by the Honored Matres. The planet's Chancellor, Reverend Mother Lucilla, manages to escape carrying the shared-minds of millions of Reverend Mothers. Lucilla is forced to land on Gammu where she seeks refuge with an underground group of Jews. The Rabbi gives Lucilla sanctuary, but to save his people from the Matres he must deliver her to them. Before doing so, he reveals Rebecca, a "wild" Reverend Mother who has gained her Other Memory without Bene Gesserit training.

Lucilla shares minds with Rebecca, who promises to take the memories of Lampadas safely back to the Sisterhood. Lucilla is then "betrayed", and taken before the Great Honored Matre Dama, who tries to persuade her to join the Honored Matres, preserving her life in exchange for Bene Gesserit secrets. The Honored Matres are particularly interested in learning to voluntarily modify their body chemistry, a skill that atrophied among the Bene Gesserit who went out into the Scattering and evolved into the Honored Matres. From this, Lucilla deduces that the greater enemy that the Matres are fleeing from is making extensive use of biological warfare. Lucilla refuses to share this knowledge with the Matres, and Dama ultimately kills her.

Back on Chapterhouse, Odrade confronts Duncan and forces him to admit that he is a Mentat, proving that he retains the memories of his many ghola lives. Meanwhile, Murbella collapses under the pressure of Bene Gesserit training, and realizes that she wants to be Bene Gesserit. Odrade believes that the Sisterhood made a mistake in fearing emotion, and that in order to evolve, they must learn to accept emotions. Murbella survives the spice agony and becomes a Reverend Mother. Odrade confronts Sheeana, discovering that Duncan and Sheeana have been allies for some time. Sheeana does not reveal that they have been considering the option of reawakening Teg's memory through imprinting, nor does Odrade discover that Sheeana has the keys to Duncan's no-ship prison.

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