The planets of the old empire have now recovered, and a new civilization has risen. There is no longer one dominant power, but three - the Ixians (the builders of no-ships capable of piloting between the stars and invisible to outside detection), the Bene Tleilax (who have learned to manufacture spice in their axlotl tanks), and the Bene Gesserit (subtle political manipulators). Lesser powers are the Spacing Guild and the Fish Speaker council.
However, circumstances are about to change, as new forces begin to make their presence felt in old worlds. People from the Scattering are returning with their own peculiar powers, secrets, and agendas. The most powerful of these forces are the Honored Matres, who are a kind of twisted Bene Gesserit, an order of women bred and trained for two purposes: combat and the sexual control of men.
Things are brought to the boil by something new arising on Rakis. Another of the God Emperor's prophecies has come to pass. A girl called Sheeana has been discovered who can control the giant worms of Rakis. The priesthood on Rakis has accepted her as holy, and the Bene Gesserit watch her development with serious interest.
The Bene Gesserit have long been waiting for this to occur. They have been buying Duncan Idaho gholas generation after generation from the Tleilaxu, in anticipation of the promised sandrider. The Sisterhood intends to use an Idaho ghola to gain control of this sandrider, and thus regain control of the religious forces of mankind. Unlike the multiple Idahos that the God Emperor used in his service, the Bene Gesserit have subtly been altering the gholas to bring their physical reflexes up to modern standards.
Upon the discovery of the sandrider, Taraza (the Mother Superior and leader of the Bene Gesserit) brings Miles Teg reluctantly out of retirement and details him to guard the new Idaho. Teg is the Mentat son of a Bene Gesserit Reverend Mother (RM), bred to serve the Sisterhood as the commanding Bashar of all their forces. Guarding Idaho is no minor task: The previous eleven gholas have all been assassinated by the Tleilaxu, the ghola providers, upon reaching adulthood. Taraza also meets with Reverend Mother Darwi Odrade and details her to take command of the Bene Gesserit keep on Rakis. Odrade is considered something of a loose cannon in the Bene Gesserit: other Sisters are suspicious of Odrade's limited prescience (inherited through her Atreides genes), an ability that manifests itself in subtle detections of threats to the Sisterhood. Further, Odrade does not obey normal Bene Gesserit prohibitions about showing emotion and the rejection of love as a "suspect" redundant human characteristic. Despite this, she is supremely talented and most suited to Taraza's needs. Making things even more complicated, Odrade is Teg's daughter.
The novel begins on Gammu (previously known as Giedi Prime, former homeworld of House Harkonnen) where the Bene Gesserit are bringing up a new Duncan Idaho ghola. RM Lucilla, a young Bene Gesserit Imprinter, has been sent by Taraza to teach this ghola and bind his loyalty to the Sisterhood. Lucilla's task is made difficult by internal divisions within the Bene Gesserit. The Sisterhood is fiercely divided on the issue of the Duncan Idaho gholas: a strong minority faction believes that they are dangerous to the Bene Gesserit, and owing to the Byzantine nature of Sisterhood politics, they have placed one of the factional leaders, RM Schwangyu, in charge of the ghola project. Lucilla has the additional agenda of repairing any damage created by Schwangyu, who has been subtly encouraging its failure, and even protecting Idaho from Schwangyu if it should prove necessary.
Ghola-Idaho has already been tarnished by Schwangyu by the time Lucilla arrives on Gammu. He nurses hate for the Bene Gesserit, hoping only to escape their control of his life. He is extremely precocious and has already divined the fact that he is a ghola.
The action shifts to a Bene Tleilax meeting in council. The Bene Tleilax are secretly an intensely religious organization who have long nursed dreams of hegemony of human space, dominating others under the weight of their religion. They are currently discussing the so-called Atreides Manifesto, an anonymous document that attacks all religions in known space, except for the Tleilaxu's. They decide to treat the Manifesto as a gift from God and spread it far and wide. The council also reveals the existence of a new breed of Face Dancer. While previous Face Dancers could only mimic the physical attributes of a desired human, the new Dancers are able to absorb the memories of another human, and use those memories to shape themselves in a perfect image of the original. Several of these new Dancers have infiltrated the highest ranks of Ixian, Guild, and Fish Speaker leadership. Additionally, the council is expecting the return of Face Dancers sent out in the Scattering hundreds of years prior. There is some mistrust of these Dancers, however, and many Tleilaxu Masters doubt that these Dancers could have maintained their purity after being exposed to the Lost Ones for so long.
After this meeting, the Tleilaxu Master Waff goes to secretly meet with the Honored Matres. The Honored Matres intend to 'mark' him and take over the Bene Tleilax, but they underestimate the little Master, and with the aid of a Face Dancer (disguised as an Honored Matre), Waff takes over the ship and kills the Honored Matres aboard. The Face Dancer reports that the Honored Matres have similar skills to the Bene Gesserit, without Other Memory, but greater sexual and fighting skills. Waff fears that the Honored Matres and Reverend Mothers might make common cause.
On Gammu, Duncan Idaho blossoms under the training of Lucilla and Teg. Schwangyu has used all her wiles to seduce Lucilla to her side but is coming to realize that she has much underestimated Lucilla.
Meanwhile, the sandrider Sheeana has been growing up among the priesthood. As a child, Sheeana's home, a village in the desert of Rakis, was destroyed by a rampaging sandworm. At the wane of the attack, Sheeana suicidally confronted the sandworm, which ceased its movements and came to rest in front of the girl. Climbing aboard the great worm as the Fremen once did, she is carried to Keen (formerly Arrakeen), where she is found by two priests. She calls the sandworms "Shaitan", not the priest-approved "Shai-hulud", which was yet another prophecy of the God Emperor. It can be noted that in Islam, Shaitan means "Accuser", and is the Etymon of the word Satan.
Her adolescence has been strange to say the least. The priesthood believe her to be holy and obey every order she gives them, though they haven't precisely decided what her role should be, and what she will become. Surprisingly she has not been too spoiled by this experience, and because there have been no constraints on her curiosity, her mind has flowed freely and well. The Bene Gesserit have also attached their own spy to her entourage, and ensure her education proceeds in the right way.
The priesthood is in turmoil on Rakis. Sheeana is approaching adulthood, and her actions and commands are putting the priesthood under increasing pressure. She persists in calling the worms Shaitan, and has banned the priesthood from certain punishments, which the priesthood have had to replace with alternative ones. All this has made Sheeana widely popular among the people, and her religious mantle has spread off world as the Bene Gesserit expected. The priesthood are split into two factions led by Tuek (the High Priest) and Stiros (leader of the conservatives).
Above Gammu, Mother Superior Taraza is willingly captured and held hostage by the Honored Matres aboard an Ixian no-ship. The Honored Matres insist Taraza invite Miles Teg to the ship, hoping to gain control of the ghola project. In an impressive display of his Mentat powers, Teg manages to turn tables on the Matres, and rescues the Mother Superior and her party as the Mother Superior had planned, though she overrides his orders to have the no-ship destroyed as they depart. Odrade is in Taraza's party, and she and Teg talk on Taraza's orders; it turns out that Odrade is one of Miles Teg's many daughters, and that it is she who wrote the Atreides Manifesto.
An attack is made on Sheeana on Rakis, which is only prevented by the intervention of the Bene Gesserit, who take unofficial control of the Priesthood and Rakis (and thus the teaching and guarding of Sheeana). Odrade, personally selected by Taraza, is now leader of the Rakis station, and she takes Sheeana under her wing, training her to be Bene Gesserit.
At about the same time an attempt is made on the life of Duncan Idaho, but Teg is able to defeat it. Realizing he can no longer protect his charge at the Bene Gesserit keep, Teg flees with Duncan and Lucilla into the countryside. With secret knowledge from his aide-de-camp Patrin, who was born on Gammu, Teg locates a forgotten Harkonnen no-globe which Patrin located as a boy. Patrin decoys the attackers, sacrificing his life so that his Bashar might live.
Taraza arranges a meeting with Waff, going into the meeting full of supposition. The Bene Gesserit have re-evaluated their records and have finally asked themselves the right questions. They have come to recognise that all they know about the Bene Tleilax is what the Tleilaxu have wanted them to know. They suspect that the Tleilaxu have been using gholas among their leaders but aren't even sure of that. Taraza gambles and blackmails Waff with the knowledge that the Bene Tleilax have killed Honored Matres, a knowledge she only has fully confirmed when she sees Waff's reaction. Waff is forced to tell her what he knows about the Honored Matres, and when pressed on the issue of Duncan Idaho admits that the Bene Tleilax have included their own agenda within him. As the meeting draws to a close, she manages by accident to divine that Waff is a secret Zensunni, which finally gives the Bene Gesserit a lever to understand their ancient competitor, and she arranges to meet Waff again on Rakis.
In the Harkonnen no-globe, Teg proceeds to awaken Idaho's original memories. Teg is facially the spitting image of Duke Leto Atreides I, (Paul Muad'Dib's father) and uses this semblance (and a variety of relentless physical and mental attacks) to awaken Duncan to his pre-death memories. He does so before Lucilla can imprint Duncan and thus tie him to the Sisterhood. Lucilla naturally is not gratified with this, and is unable to use her wiles to imprint Duncan afterward, because the now-awoken Idaho is aware of her agenda. Duncan even tells her that if she tries it, he will attempt to kill her.
Waff meets Odrade on Rakis. In a meeting with Tuek and Odrade, he panics and tries to assassinate them both; while he succeeds in killing the unsuspecting Tuek, Odrade is too clever for him, and not only dodges his attack but shatters both his arms in a counterattack. Odrade turns the tables on Waff, using knowledge Taraza gained from her meeting with Waff to partially convince him that the Sisterhood shares the religious beliefs of the Bene Tleilax. Waff and Odrade install a new Face Dancer as a replacement Tuek, as the alternatives would be too inconvenient.
In the meantime Taraza, via Teg's finest pupil Burzmali, has been searching for Teg and his party, having little success. But finally, in a flash of inspiration, Burzmali realizes where Teg must be, and establishes contact with him and arranges to bring his party to safety. During the extraction operation, however, Teg and his companions are ambushed. Teg sacrifices himself to capture while Lucilla and Duncan escape with Burzmali.
Odrade decides it would be a good idea to put Waff under pressure and so she arranges a sandworm ride into the desert with Sheeana. The worm, influenced by the God Emperor's "pearl of consciousness" trapped within it, takes the passenger to the former Sietch Tabr, where Odrade finds a secret Spice hoard and a message sent down through time from the God Emperor. This message challenges the Bene Gesserit to abandon their secret ways and openly protect Leto's Golden Path. Leto particularly maligns the Sisterhood's lack of "noble purpose," an attack that strikes Odrade deeply.
Odrade takes it upon herself to offer full alliance with the Bene Tleilax, in the face of the onslaught of forces out of the Scattering. The cement for this alliance is Waff's belief that the Sisterhood shares his Tleilax religion, which sees Leto as a Prophet from God. Part of the alliance promises Bene Gesserit breeding Sisters for the Tleilaxu to work into their ghola breeding programs; as compensation, the Sisterhood will receive a working axlotl tank for their own purposes. This agreement causes consternation among the Bene Gesserit. Some call for Odrade to be assassinated. Taraza worries over this and then decides to go to Rakis to decide whether to follow Odrade's course, or to kill her.
On Gammu, Teg is interrogated and tortured using a T-Probe, and under the pressure of the experience discovers a new ability in his Atreides heritage: he is able to speed up his physical and mental reactions to lightning speeds, enabling him to escape his bonds and kill everyone imprisoning him. After this acceleration, however, Teg requires massive amounts of food to replenish his lost energy. At the same time, Duncan Idaho, who is attempting to get off of Gammu undetected in the guise of a Tleilaxu Master, is ambushed and taken hostage.
Meanwhile on Rakis, Taraza has come for her inspection. She is worried that Odrade may need to be killed, but on arrival realizes that Odrade has seen her real plan and is merely following it in her own creative way. Taraza seeks the destruction of Dune, because she believes the God Emperor still binds humankind on a particular course through the sandworms of Rakis; Taraza wishes to free humanity to follow its own possibilities. With the destruction of Rakis, the Bene Gesserit would be totally dependent on the Tleilaxu for the Spice they utterly need, so alliance with the Tleilaxu would ensure their supply. Taraza evaluates Sheeana and is impressed with what she sees, and this raises the possibility of the Bene Gesserit following a secondary plan of seeding other planets with worms transported by the sandrider. In an interview with Taraza, Waff discovers he cannot control his Tuek Face Dancer - its copying is so perfect it has forgotten it is actually a Face Dancer. Taraza uses the moment to confirm her alliance with the Bene Tleilax.
By this time Lucilla and Burzmali arrive at a Bene Gesserit safe house to discover it has been taken over by Honored Matres. Luckily, the young Honored Matre, Murbella, stationed at the safe house is fooled by Lucilla's stolen Honored Matres robe, and accepts her as an observer. Murbella proceeds to seduce the captured Duncan Idaho. However, as she starts the seduction procedure, hidden Tleilaxu conditioning kicks into action and Duncan responds with an equal technique, one that overwhelms Murbella in sexual pleasure, draining her energy. Overwhelmed with a desire to feel such euphoria again, Murbella finds herself unable to kill Duncan, though she recognizes the danger he poses to the Matres. Taking advantage of Murbella's post-coital exhaustion, Lucilla knocks her unconscious.
The Honored Matres finally attack Rakis. Taraza is killed with the first attack, cut down by lasguns. Odrade has time to merge minds with her, becoming temporary leader of the Bene Gesserit, before escaping with Sheeana into the desert on a worm.
Eluding capture for a while Teg finally goes to a supposed safe house, only to discover that it has been taken over by the Honored Matres. Meeting them in person Teg is disgusted by their corruption and complete lack of human decency. The Honored Matres have assessed Teg's value to their order and decide to 'mark' him, binding him to their designs. Teg, aware of his new abilities, waits for the chosen Honored Matre to come to collect him, and then unleashes himself upon the complex.
Teg must seek his own allies in order to escape Gammu. He finds a groups of ex-soldiers who have formed a resistance group to the Honored Matres. He brings them together and attacks a no-ship, and captures it. He locates Duncan and Lucilla, and with the captured Honored Matre, takes them to Rakis.
Teg arrives at this time and with his new vision finds Odrade and Sheeana and their giant worm. He loads them all up in his no-ship, finally leading his troops out on a last suicidal defence of Rakis, designed to attract the rage of the Honored Matres. Fulfilling Taraza's designs, the Honored Matres attack Rakis in full force, destroying the planet and the sandworms. With this attack, the Matres hoped only to destroy Teg, whose abilities they had witnessed through his escape from their Gammu complex. The giant worms are destroyed bar the one the Bene Gesserit escape with. They drown the worm in a mixture of spice and water killing the worm and turning it into sandtrout which will turn Chapterhouse into another Dune. Taraza's camp is proven right: the God Emperor did wish to be freed from his existence, and he did not prevent them from destroying Dune. As we leave the book Odrade is the precarious temporary leader of the Bene Gesserit, by virtue of being at the right place at the right time having inherited Taraza's memories.