Quick setup: In the year 10000-something, humanity has spread across the known universe after the discovery of a substance known as the Spice Melange on the planet Arrakis which enables those who imbibe it to enter a trance like state that allows them to peer into the future. This facilitates space travel as Navigators can use it to see safe paths through the stars. This makes Spice the most important substance in the universe and Arrakis the most important planet in the universe, as there are no other sources of Spice.
The story starts with a 15 year old named Paul on a normal planet called Caladan. He is the prince of House Atreides, and has strange dreams about his future on the desert planet Arrakis. His mother Jessica is part of an ancient sisterhood called the Bene Gesserit who have been planning and executing a eugenics-like breeding program for thousands of years in order to bring together the correct combination of genes that will produce the one they refer to as the "Kwisatz Haderach" or, the one who can be many places at once. Essentially a person who can see the future, the past, and the present with total omniscience. They believe Paul might be the one.
In preparation for this, the Bene Gesserit have planned many schemes over they years. One of which involved planting a religious legend among the natives of Arrakis, the Fremen. The Fremen come to completely believe this as truth when House Atreides comes to Arrakis and Paul is revealed to them. During the course of the first book, House Atreides is betrayed by the Emperor to the Harkonnens, who are basically just comically evil in every way. This leaves Paul and his mother Jessica the only survivors, and they flee into the desert. They meet the Fremen, who have mastered the art of survival in the harshest of environments, and are accepted by them. Eventually, they come to see Paul as the one from the old Bene Gesserit planted religious legend - they see him as a literal messiah who will lead them into a new golden age. They deify him and follow him without question. Under his leadership, they rout the oppressive Harkonnens, defeat the Emperor, and Paul himself takes the imperial throne for himself. The end... right? Wrong.
All along the story, Paul has been having visions of the future, because he truly is the Kwisatz Haderach. He can see into his ancestors' past, he can compute instantly what will happen in the present, and he can see into the future with the Spice trance. And what he sees is a bloody jihad by the Fremen that he will lead across the universe, slaughtering billions. He tries as hard as he can to avoid it, but in the end he cannot avoid his terrible fate. He succeeds in freeing the Fremen from the Harkonnens and the Imperium, but what happens afterwards is exactly as he has forseen. His ruthless death commandos spread across the universe killing some 60 billion people in his name, and because of the intricacies of Fremen law, culture, and religion, he cannot easily stop the jihad. Eventually he figures out the way to stop it, but this involves blinding himself, exiling himself into the desert, and eventually discrediting his own godhood, tearing down the very religion that he used to defeat the Harkonnens in the first place.