Paul Muad'Dib leads the mighty Fremen warriors against those trying to take Dune for themselves. They attack the Harkonnens and spice miners to stop the production of spice. This forces the Emperor to come to Dune and take control of the situation. Riding across the desert on the great sandworms, the Fremon defeat the forces of the Harkonnens and the Imperium, and Muad'Dib assumes the throne as Emperor.
On Dune, Paul is approched by a race called the Tleilaxu. They bring with them a very unusual gift, they have brought Paul's friend, Duncan Idaho, back to life. Duncan was killed by the Harkonnens, and now lives on as a clone. But this meeting turns out to be part of a conspiricy between the Tleilaxu, the Spacing Guild, and the Bene Gesserit to destroy Paul and take control of the Imperium.
Paul later finds himself overwelmed by powerful visions of himself and his future. These visions are all he sees after an explosion takes away his eyes. As the conspiricy plays out, Chani, Paul's lover, is killed. She gives birth to Paul's twin children just before she dies. The assassination attempt on Paul's own life, and his children, fails. In the end, Paul's visions stop and he is left totally blind. He turns leadership of the Imperium over to his sister, Alia, until his son is old enough to rule. Then, in the tradition of the Fremen, he is left out in the desert to die.
Members of the old House Corrino set up a plot to kill the twins and restore their house to the Imperial throne. Ghenima survies the attack on her and her brother. However, it appears that Leto is killed. After faking his own death, Leto journeys into the desert to seek out his destiny. There he joins with the great sandworms of Dune. He begins a tranformation that would allow him to live for thousands of years as he becomes part man part sandworm. This would also give him enought time to carry out his "Golden Path" In the desert, he also encounters a blind preacher, who turns out to be his father, Paul Muad'Dib, who has survived out in the desert.
Paul and Leto return to the city of Arrakeen to confront Regent Alia. She has been possesed by the spirit of the dead Baron Harkonnen. Paul speaks out against her, and is killed by a religious fanatic. Alia, in turn, kills herself, rather than let herself be contorled by the evil Baron. Leto is made Emperor with Ghenima by his side. Leto's "Golden Path" begins.
There are many that oppose the God Emperor. Among them is Siona, an resistance fighter and a decendent of House Atreides. She is the daughter of the Emperior's top advisor and seeks to end the tyrant's reign and free her father. She is joined by another clone of Duncan Idaho. Throughout his reign, Leto has cloned Duncan over and over again to be his servant. This Duncan refuses to bow to the tyrant's wishes. Other forces also seek to take Leto's control away from him. Both the Guild and the Tleilaxu work to come up with an alternative form of space travel that doesn't require spice. And the citizens of the planet Ix have their own method of controling the Emperor, with the perfect companion.
The first time Leto meets the Ixian ambassador, Hwi Noree, he immediately falls in love with her. Although, he is far from human, Hwi seems to share similar feelings for the Emperor. Well aware that she was bred specifically to distract and control him, he can't help but love her and Hwi can't stand the thought of hurting him. They agree to get married. It is during the wedding procession that Siona and Duncan attack. The entire procession is killed, including Hwi, and the God Emperor. Leto knew he would have to sacrifice himself for the good of humanity. His death is all part of the "Golden Path" and as he dies, the part of him that was sandworm begins to turn Dune back into a desert planet.
While trying to find a way to combat this great threat, the Sisterhood makes two important discoveries. On Dune, they find a girl named Sheeana, who possesses the ability to control the great sandworms. And, locked away in a Bene Gesserit stronghold, a young boy hold's the key to their victory. This boy is another clone of the long dead Duncan Idaho, and his creators have given him the secret knowledge of how to overpower an Honored Matre.
After a great battle, the planet Dune is destroyed. But, the Bene Gesserit have gained control of the last surviving sandwarm. They use its power to turn their own planet, Chapterhouse, into a new Dune. They have also captured an Honored Matre named Murbella. They try to break her away from her Honored Matre ways and train her as a Bene Gesserit Reverend Mother. Nearing defeat, the Bene Gesserit gather their forces and launch an attack on the Honored Matres. Another great battle is fought, and in the end, Murbella kills the Honored Matre leader and gains control of both the Honored Matres and the Sisterhood. She unifies the two warring factions in an alliance that would change the universe forever.
Although, this description gives quite a bit of detail into these stroies, there is so much more that happens. These book are so detailed and the story is so vast that it would take a long time to explain everything. These are still only some of the elements of this phenomenal series.