The book is divided into seven sections, which alternate in time between the beginning and midway through the period of Muad'Dib's Fremen Jihad and a period in the youth of Paul Atreides, several years before the events portrayed in Dune.
The book further chronicles the life of Paul Atreides in two different parts—five years before House Atreides moved to Arrakis, and their involvement at that time in the War of Assassins of 10,187 AG. The second part of the book involves the life of Muad'Dib, and the immediate years after his ascension as Emperor of the Known Universe.
Paul on Caladan
Paul of Dune begins with the Emperor Paul Atreides' Jihadi forces scattered through the Imperium, fighting the rebel houses that refused to recognize him as Emperor. While Paul visited Caladan with his mother, the Lady Jessica Atreides, and his appointed temporary suzerain of the water world, Prince Xidd Orlaq, Paul was presented with the good news that the Fedaykin have captured Kaitain. Paul immediately installed his mother as Duchess of Caladan, and departed on the next heighliner to the former Corrino capital.
Alia Reigning on Arrakis
While Paul was gone to Caladan, he left his four year old sister, Alia, as acting ruler in his stead. Alia received ambassadors from the Guild, Ertun, Loyxo, and Crozeed, who of course, begged for more melange, for the space-faring organization. Alia, wisely, told them that the Guild could have 3% more spice annually if they would contribute 200 more heighliners to Paul's Jihad.
She also watched as Korba, Paul’s chief aide and counselor, killed and dispatched the former Emperor Shaddam’s chamberlain, Beely Ridondo. The Corrino servant had gone to Arrakis from Salusa Secundus to petition the Emperor and his court, to terra-form the nuclear devastated world as he promised when Shaddam was deposed a year earlier.
The Corrino Plot
On Salusa Secundus, the former Imperial ruler, Shaddam, gave the Emperor's Blade to his Sardaukar chieftain, Zum Garon, and charted him with the task of finding his former childhood friend, the former Count Hasimir Fenring, and bringin him back to the devastated planet. Garon’s travels led him to Thalidei, on the planet Tleilax, where Fenring, his wife Margot, and their daughter Marie, were taking refuge. Garon gave Fenring the Emperor’s Blade, but Fenring replied that he would have to think about rejoining the former Emperor.
Paul on Kaitain
When Paul arrived on Kaitain, Paul allowed the former Emperor Shaddam IV's Palace to be demolished and destroyed by the over-eager Fremen, the news of which he knew would spread throughout the galaxies as a warning to rebels. Soon afterwards, Paul addressed the hastily gathered Landsraad, and informed them that tariffs and penalties will be imposed upon dissident Houses that did not bow to his will. During the banter during the question and answer session after the Emperor’s speech at the great Oratory hall; Earl Memnon Thorvald addressed the Known Universe’s assembly, and vowed to all gathered that he would nor would a great deal of others bow to another mad and misguided Emperor, and then stormed out.
Afterward, when Paul left the Lansraad gathering with Princess Irulan, Paul met his old recognized friend, the Swordmaster of Ginaz Whitmore Bludd, who was in the service of House Ecaz and was a friend to Paul's former mentor, Duncan Idaho. Bludd, who had knowledge of architecture, was asked by Paul to help him construct the grandest palace and citadel in the universe, in Arrakeen on Arrakis, to which Bludd agreed and accompanied him back to Dune.
The Wedding of Leto & Ilesa Ecaz
When Paul was twelve years old and living on Caladan, the Ecazi-House Moritani conflict had been going on for many years involving the heads of each respective Great House. Paul was embroiled in this famous War of Assassins conflict, during which he had to mature rapidly in order to deal with all the challenges that it possessed for House Atreides.
Paul and his mother Jessica were brought to the planet Ecaz aboard a guild heighliner along with Duke Leto and his retinue. There, a marriage deal was concluded between Armand Ecaz and the Atreides for Duke Leto to marry Ilesa Ecaz, the Archduke’s youngest daughter. The marriage was prompted by political decisions: House Ecaz needed allies to fight against the Moritani aggression, and House Atreides fitted the bill perfectly, since Leto had actively condemned the actions of House Moritani and officially formalized the Atreides-Ecaz alliance.
Duke Leto and Illesa’s wedding was to be held at Castle Caladan. Decorations included potted plants of Ecazi origin, given as a gift by Duke Prad Vidal, which turned out to be concealing cleverly placed iron shards. The pots cracked and out shot the iron shards, killing Swordmaster Rivvy Dinari in the service of Ecaz. Other flying shard discs caused the Archduke to lose an arm, and Swordmaster Whitmore Bludd, not reacting fast enough to the threat, could not prevent the death of bride-to-be Ilesa. Later that day, two Moritani assassins entered Castle Caladan. and tried to assassinate Paul and the young heir of House Vernius, Bronso.
Meanwhile, Earl Thorvald, the nobleman who is heading the rebel forces, is being chased by Stilgar and the Feydaykin across the galaxy. Elsewhere, the exiled Count Fenring and Margot have raised their daughter, Marie, on Tlielaxu to become a weapon, and she progresses steadily in training.
Assassination of Prad Vidal
Brimming with hatred for his arch-enemy, Hundro Moritani, Ecaz decided to mount a full-scale offensive against House Moritani, and asked House Atreides to join him. The Archduke promised to pay half of the costs of the military operation for House Atreides. The Atreides military departed on aheighliner toward Ecaz, where the Archduke realized that the upstart duke, Vidal, had taken over the reins of the government. Duke Leto and Duncan Idaho stealthily moved into the Ecaz palace and kill Prad, and allowed the Archduke to re-take his homeworld and assemble his forces.
First Assassination Attempt on Muad'Dib
More and more Houses are joining Thorvald's movement due to the savage brutality of the Fremen. Bludd is executed after the Swordmaster tried to assassinate Paul to make his mark in history.
Battle of Grumman
The combined Atreides-Ecaz military forces were transported to the planet Grumman. Landing, the Atreides-Ecaz forces rushed to battle against the Moritani and concealed House Harkonnen forces provided by Baron Vladimir Harkonnen. The head of House Moritani had prepared a trap for the Atreides-Ecaz forces, but because of a foolish decision by Rabban Harkonnen, most of the Grumman and Ecaz forces fell into a deep pit outside the capital city of Ritka. The pit had been created by detonations in underground tunnels dug many years ago by Moritani to strip the earth for ores.
Finally, a heighliner transporting Imperial Sardaukar and the Emperor Shaddam Corrino IV arrived to prevent full-scale war. The whole offensive was actually grand plan by Hundro to annihilate the Ecaz, Atreides and Imperial forces together by using a doomsday weapon. The plan failed when the weapon failed to detonate as the Grumman Swordmaster Hih Resser had disabled the weapon, finally bringing the entire conflict to a close.
Defeat of Thorvald
Paul had a prescient vision that Thorvald and his forces were going to attack Caladan, and Paul comes to the conclusion that only sterilization will make his enemies bend to his will. Paul ordered a complete annihilation of Earl Thorvald's home planet, Ipyr, which rendered the world sterile and lifeless.
Second Assassination Attempt on Muad'Dib
As Marie had been strategically placed in the Imperial Court, the Fenrings unleashed their plan. While Marie failed and gets killed by Alia, Fenring managed to plunge the Emperor's Blade through Paul, and near-killed him for several hours. Upon his awakening, Paul did the unthinkable: he forgave Fenring and exiled him and Margot to Salusa Secundus to spend the rest of his life with his former master Shaddam, whom the Count loathed.