Warning: Wikipedia contains spoilers
At the end of Dune (novel), Paul Atreides is triumphant, but we find in Dune Messiah twelve years on that this triumph has not brought Paul the Empire he would have wanted. He won the Fremen to his side by using the religious card, but having started a jihad he discovers it is impossible to stop, and the Fremen have taken their religion everywhere he sends them in the Empire. So Paul sits on an empire in a more powerful position than any Emperor before him, but finds himself powerless to stop the excesses of the juggernaut he has created.
His jihad has killed sixty billion people across the known universe, but according to his prescient visions, this is a fate far better than others he has seen. Paul is beleaguered by the need he sees to set humanity on a course that doesn't lead to its stagnation and destruction, while at the same time managing both an empire and a church built around him.
Paul has had no children. Chani, his lover has not conceived because Princess Irulan has been secretly feeding her contraceptives. Paul is aware of this, but he has seen in his visions that for Chani giving birth will cause her death, so he lets the situation continue as it is, because he does not want to lose her. Chani, however, changes the dynamic at this point by deciding to go on a traditional spice diet in an attempt to have children. Irulan is unable to meddle with this diet and Chani soon becomes pregnant.
The conspirators who plot his doom are a varied bunch: Gaius Mohiam, representing the Bene Gesserit, who wish to regain control of their breeding programme; Edric, a guild navigator representing the Spacing Guild, and by virtue of his own oracular powers, protects the conspirators from Paul's visions; Scytale, a face dancer representing the Bene Tleixiau; and Irulan, their spy in the Emperor's household who wishes to be mother to a dynasty. The conspirators plan is a subtle one; it begins with the Spacing Guild giving Paul a gift he cannot resist, a ghola of Duncan Idaho, his childhood teacher and friend. The conspirators send Hayt -the ghola - in the belief Paul will be undermined with doubt because Hayt will make Paul question himself and the empire he has created.
The arrival of the ghola creates shock waves. Paul is unable to refuse this gift, and so gains to his service a Mentat trained philosopher and swordsman. This action weakens Paul's support among the Fremen because they see the Tleilaxu and their tools as unclean. Mennwhile Alia, his sister, is also most taken with him, her body has now reached puberty and screams for a worthy mate.
Soon after a dead woman is found near the city. Alia and Hayt investigate, and do not learn much. However, Hayt realizes that it means a Tleilaxu plot, because no woman has been reported missing by any Fremen in the city; she is probably not missing because she has been replaced by a face dancer. Hayt also takes this opportunity to steal a kiss from Alia. She outraged, but Hayt just laughs, saying he took nothing more than she offered, a fact she admits to herself privately.
Mohiam, the Reverend Mother is called to an audience with Paul Maud'dib. She enters worrying that it might mean her death, but she is soon elated by the knowledge that he wants to bargain with her. What Paul offers is utterly cunning. He offers a child of his by artificial insemination in return for Chani's survival, and her child. Mohiam is caught between conflicting pressures. On the one hand the Bene Gesserit are desperate to regain the Atreides genes for their breeding programme, but on the other artificial insemination breaks the Butlerian taboos against the use of machines. It has the further effect that no child born that way would be a candidate for the Imperial throne, and the Bene Gesserit could not even admit this child existed without weakening their own moral position in the Empire. She decides that she must consult with the Mother School of the Bene Gesserit on Wallach IX about a decision of such significance.
Six weeks later Chani is seen by a medic about her pregnancy. She is upset to discover why her pregnancy has complications: that someone has been feeding her contraceptives, obviously Irulan, and that this is going to make her pregnancy dangerous. Chani wishes to kill Irulan, but Paul tells her that it will not help. Chani takes this to be a prophetic vision and such is her trust in Paul that she regains her balance. She then realizes that Paul has been sparring with Hayt and questions whether it is sensible for Paul to do this. Paul answers that the Tleilaxu have made better than they could know, that he is also Duncan Idaho, and suggests that it may be possible to restore Hayt's memories as Duncan Idaho.
Later, a daughter of one of Paul's death commandos - Otheym - arrives, asking Paul to visit her father secretly. Paul is aware that the woman is really a face dancer but we learn he is hemmed in by the alternatives he sees in his future. Revealing that it is a face dancer leads to futures he does not want, so he plays along with the obvious conspiracy. The face dancer asks to be taken into Paul's household for safety, and Paul concurs.
Paul visits Otheym, and is pleased to discover that his old comrade is still himself but obviously unaware his daughter has been replaced with a face dancer. Otheym reveals that he has discovered a huge plot against Maud'dib among Fremen, and that he has the evidence against them. He has a Tleilaxu servant, who is like a recording machine, and he can relay faces, names and conversations on command. Otheym gives Paul his servant Bijaz, and Paul accepts reluctantly, knowing full well that he is entering into some sort of Tleilaxu plot.
The plot is soon revealed. As Paul's soldiers attack the source of the conspiracy against him, Otheym's house explodes viciously. The Tleilaxu set off a stone burner, destroying the house and blinding many people nearby, including Paul. Although physically blinded, Paul is able to continue in leadership because his oracular powers allow him to see the world around him.
Paul is aware of many of the conspirators now. Included with them is Korba, high priest of Paul's church. Korba tries to deny all part in the plot, claiming that while the Qizarate did procure the Stoneburner, it was stolen without his knowledge. Korba is reasonably successful in persuading the Naibs of his innocence, until Paul arrives to confront him directly. The meeting ends with Korba being put into the custody of Stilgar, who promised to discover the truth.
Bijaz is questioned by Hayt. This was foolish because Bijaz uses planted conditioning words to control Hayt. He programs Hayt to offer Paul a bargain when Chani dies. Bijaz offers Chani's return as a ghola, in return for Paul sacrificing the throne and going into exile. Bijaz also betrays the hope that Duncan Idaho might be woken. Bijaz then commands Hayt to forget the conversation.
Hayt comes across Alia after she has taken a huge dose of spice in the hope of enhancing her prophetic visions. She is delirious and in danger of dying provoking a fierce emotional response from Duncan at the thought of an Atreides dying. He rushes her to a medic. During the experience Alia realizes that Duncan loves her. She asks him if this is so, and he admits it.
Paul and Hayt are talking when news is brought that Chani has died giving birth to two children, who are both fine. This message and Paul's reaction to it, trigger the hidden compulsions in Hayt's mind, and he attempts to kill Paul. But his body reacts against his programming and remembers itself, and a new consciousness arises, a mix of Duncan Idaho and Hayt, which is unconditioned by the Tleilaxu programming. Paul asks if it Duncan Idaho himself again, and Duncan answers yes. Paul is unsurprised by this as he saw it in a vision.
They go to say goodbye to Chani, and see her newborn children, only for there to be a standoff. Along the way Paul's prophetic vision fails, he reached the key decision point in time, a spot where not even he could predict all the consequences, and he becomes truly blind. Scytale, disguised as Otheym's daughter, holds a knife to the necks of Paul's children. He offers Paul a poisoned chalice. He will give Paul a ghola of his beloved Chani, if he will hand over power, while at the same time he threatens the lives of Paul's children. Paul finds vision from an unusual source, he is able to see through the eyes of his newborn son, and is able to throw a dagger and kill Scytale.
Paul, however is now truly blind. He makes Alia regent for his children.
and then he chooses to walk off into the desert as blind Fremen do, and so cements his family's power among the Fremen.
The book ends with Duncan musing. He examines the irony that despite the fact Paul is dead, as is his love, Chani, Paul has triumphed against his enemies. He escaped deification, it was as a man that he walked into the desert, not as a god. His enemies have over-reached and a pogrom, initiated by Alia, Stilgar, and the vengeful Fremen, leads to their end. Indeed, by walking into the desert as according to Fremen tradition Paul has won the fealty of the Fremen for his children who will inherit his mantle of Empire, with regenthood being Alia's until they are adults. Stilgar interrupts Duncan to suggest he should go to a distraught Alia who need his support. Duncan goes to comfort Alia and they swap professions of love. The Atreides empire seems to be in good and secure hands.
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