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Dune Messiah is a science fiction novel by Frank Herbert, the second in a series of six novels. It was originally serialized in Galaxy magazine in 1969. The American and British editions have different prologues summarizing events in the previous novel. The novels Dune Messiah and Children of Dune were adapted by the Sci-Fi Channel in 2003 into a well-received mini-series entitled Children of Dune.
Twelve years after the events described in Dune, Paul Atreides rules as Emperor of the Known Universe, following a galactic jihad he unleashed by accepting the role of Messiah to the Fremen. While Paul is the most powerful Emperor ever, he is ironically powerless to stop the lethal religious excesses of the juggernaut he has created.
Although sixty billion people have perished, Paul's prescient visions indicate that this is far from the worst possible outcome for humanity. Motivated by this knowledge, Paul hopes to set humanity on a course that will not inevitably lead to stagnation and destruction, while at the same time acting as ruler of the Empire and focal point of the Fremen religion.
The situation is further complicated by the conspiracy of powerful interests who hope to reverse the events that brought House Atreides to the throne, including the remnants of the displaced House Corrino, the Bene Gesserit who have lost control of their Kwisatz Haderach, the Spacing Guild, now utterly beholden to Paul, and the Bene Tleilax. The Atreides dynasty is unstable because Paul has not produced an heir. Chani, his lover, is secretly being given contraceptives by the Princess Irulan, and while Paul is aware of this, he has foreseen that the birth of his heir will bring Chani's death, and he does not want to lose her. Chani then conceives after switching to a spice-only diet.
The conspirators, including a Bene Gesserit Gaius Helen Mohiam, Edric a spacing guild navigator, Scytale a Tleilaxu face dancer, and Princess Irulan, give Paul a gift he cannot resist, a ghola of Duncan Idaho, his childhood teacher and friend, now called "Hayt." The conspirators hope the presence of Hayt will undermine Paul's ability to rule by forcing Paul to question himself and his empire he has created. Furthermore, Paul's acceptance of the gift weakens Paul's support among the Fremen who see the Tleilaxu and their tools as unclean.
Further complicating the situation is the physical maturity of Paul's powerful sister, Alia, who finds herself irresistibly attracted to Hayt/Duncan. Alia and Hayt investigate the appearance of a female corpse near the city; Hayt realizes that the fact that no-one has been reported missing implies a Tleilaxu plot in which the woman has been replaced by a face dancer. Hayt also takes this opportunity to steal a kiss from Alia. She is outraged, but Hayt just laughs, saying he took nothing more than she offered, a fact she admits to herself privately.
Paul Muad'dib demands to see Mohiam, who fears she will be killed, but instead discovers Paul wants to bargain with her: Paul offers to produce a child by artificial insemination in return for the survival of Chani and her child. Mohiam, desperate to regain the Atreides genes for the Bene Gesserit breeding programme, would have to violate the Butlerian taboos against the use of machines. Furthermore, she realizes no child born in this way would be a candidate for the Imperial throne, and that the Bene Gesserit could never admit the existence of such a child without risking their position in the Empire. She decides that she must consult with the Mother School of the Bene Gesserit on Wallach IX.
Six weeks later Chani is seen by a medic, and discovers her pregnancy has become complicated because of the contraceptives introduced to her system. Realizing that only Irulan could be the perpetrator, Chani wishes to kill her but is prevented by Paul. She questions whether it is sensible for Paul to continue to spar with Hayt, and Paul replies that the Tleilaxu have made better than they could know and that it may be possible to restore Hayt's memories as Duncan Idaho.
The daughter of Otheym, one of Paul's death commandos, asks Paul to visit her father in secret, and while Paul realizes she has been replaced by a face dancer, his prescient visions show that revealing this will lead to futures he wishes to avoid. Paul is forced to admit the face dancer asks to be taken into Paul's household, and visits Otheym.
Otheym reveals evidence of a conspiracy against Muad'dib among the Fremen, some of whom are distrustful of following the Atreides, and gives Paul his Tleilaxu servant Bijaz, who like a recording machine can remember faces, names, and details. Paul accepts reluctantly, seeing the strands of a Tleilaxu plot. As Paul's soldiers attack the conspirators, the Tleilaxu set off a stone burner, an atomic weapon that destroys the house and blinds Paul. Paul is able to continue in leadership by fixing his actions precisely in line with what his previous oracular visions showed him; by moving through his life in lockstep with his previous visions, he can see even the slightest details of the world around him. The disadvantage of this is his inability to change any part of his destiny so long as he wishes to appear sighted.
The unraveling of the conspiracy reveals that Korba, high priest of Paul's church, is among Paul's enemies, and while Korba tries to deny this, persuading the Fremen Naibs of his innocence, Paul arrives to confront him directly and Korba is put into Stilgar's custody.
Hayt interrogates Bijaz but Bijaz uses planted conditioning words to control the ghola, and programs Hayt to offer Paul a bargain when Chani dies: Bijaz offers Chani's return as a ghola, and the hope that Duncan Idaho might be reawakened, in return for Paul sacrificing the throne and going into exile. Hayt comes across Alia, who has overdosed herself with spice in the hope of enhancing her prophetic visions. Her peril provokes fierce emotional response from Duncan and Alia realizes that Duncan loves her; he admits the truth.
News is brought that Chani has died giving birth to two healthy children, Leto and Ghanima, pre-born (fully conscious with Kwisatz Haderach-like access to ancestral memories due to Chani's encounter with the spice essence while pregnant with the twins) like their aunt Alia. News of the birth is delivered to Paul and his reaction to it triggers the hidden compulsions in Hayt's mind, and he attempts to kill Paul. Reacting against its own programming, Hayt's body remembers itself, and a new consciousness arises that is a mix of Duncan Idaho and Hayt unconditioned by the Tleilaxu programming. Paul is unsurprised by this, having foreseen it.
As Paul nears a crucial decision point in time, causing his prophetic visions to fail and rendering him totally blind, he is thrust into a deadly standoff. Scytale, disguised as Otheym's daughter, holds a knife to the necks of Paul's children. He offers to revive Chani as a ghola in return for Paul's abdication. Paul receives a prescient vision from the perspective of his newborn son, and is able to throw a dagger and kill Scytale.
With Paul's visions gone, he chooses to walk into the desert in the Fremen tradition, winning the fealty of the Fremen for his children, who will inherit his mantle of Emperor. Paul leaves Alia as regent for his children.
At the conclusion of the novel, Duncan examines the irony that Paul and Chani's deaths enabled them to triumph against their enemies. Duncan realizes that Paul escaped deification, walking into the desert as a man, while guaranteeing Fremen support for the Atreides line. Stilgar interrupts Duncan to suggest he should go to a distraught Alia, and Duncan goes to comfort her. Before Idaho goes to comfort Alia, Stilgar reports that he has carried out Alia's orders to execute Gaius Helen Mohiam, Edric, Korba, and "a few others." Because the key players of the conspiracy are now dead, Paul's children are left in a relatively safe situation. With Paul's family secure and his most trusted associates in power, the Empire and House Atreides appear to be in safe hands.