Book I: Dune
Fearing the rising popularity of Duke Leto Atreides, Emperor Corrino plots with Baron Vladimir Harkonnen to have the Atreides family annihilated. The plan is about as convoluted and intricate as a Rube Goldberg machine, but here we go all the same.
The Emperor will secretly grant the Baron the use of his elite death commandos, the Sardaukar. At the same time, the Baron will use the centuries-old feud between the Houses to openly attack the Atreides. He'll also convince one of Leto's most trusted lieutenants to turn traitor while placing the blame on his lover, Lady Jessica. The theater for Duke Leto's grand destruction will be none other than the desert planet of Arrakis, a.k.a. Dune. Whew, did you get all that?
There's only one thing they didn't consider: Paul Atreides, Duke Leto's only son. One week before leaving for Arrakis, Paul is visited by the Bene Gesserit Reverend Mother Gauius Helen Mohiam, or, as we like to call her, the Reverend Mother. She tests Paul using the gom jabbar, a deadly coming of age ritual. Paul passes the test, but little does he know that this ritual is the beginning of his path toward becoming the Kwisatz Haderach—a.k.a. a guy with a ridiculous name but equally ridiculous powers.
On Arrakis, Duke Leto tries to gain "desert power" to fight off the inevitable Harkonnen invasion. The keys to his plan are the Arrakis aboriginal tribe called the Fremen—a civilization trained like the Marines—and the spice, a mind-bending drug required for civilization to thrive in the universe. Leto's attempts are valiant, but Dr. Yueh betrays him before his plans can come to fruition. Yueh and Leto conspire to kill the Baron, but they fail. The Harkonnens conquer Arrakis, destroy the Atreides, and control the spice trade. The end.
Book II: Muad'Dib
Or it would be the end, if not for the fact that Paul and Jessica evade the Harkonnens' grasp. Although they lose many allies along the way, Paul and Jessica eventually escape to the south desert. There, they find a Fremen tribe led by a man named Stilgar. Using their weirding powers, Paul and Jessica convince the Fremen they are messianic figures from Fremen religious myths, and they are invited to stay. After all, it's just rude to not ask the messiahs in for coffee, especially when they are prophesized to make your planet a paradise.
A Fremen named Jamis challenges Paul to a duel, hoping to prove that Jessica is a poser. When Paul kills Jamis fair-and-square, he is adopted into the tribe and give the name Muad'Dib, a name Paul's dreams suggest will bring about a universe-wide jihad. Bummer. On the plus side, Paul gets a Fremen girlfriend named Chani, so you take the good with the bad.
Jessica has to prove herself another way. She consumes the Water of Life and gains the collective memories of the Fremen. This officially makes her the Fremen's Reverend Mother, and she takes a new position as spiritual leader among the tribes. She also learns the truth about the spice and how the Fremen control it.
Paul and Jessica become members of Fremen society where they live happily ever after. The end.
Book III: The Prophet
Okay, fine. They live happily, but not quite ever after.
A few years later, Paul passes his test into manhood and learns how to ride the worms. Yes, you read that right. After the test, he runs into his old teacher, the master warrior Gurney Halleck. There's a bit of a scuffle when Gurney tries to kill Jessica, believing her to be a traitor. But they work it out in the end. No feelings hurt; no knives in anyone's back.
With Gurney and Stilgar at his side, Paul decides it's time to put his plan into action. He drinks the Water of Life and becomes the Kwisatz Haderach for reals. Then he rallies all the Fremen tribes under his banner and begins his war against the Harkonnens.
Worried about the spice, the Emperor, the Spacing Guild, and the Harkonnens land on Arrakis to counter Paul's assault. Bad move. Paul's Fremen know Arrakis and use the worms and even the weather against their opposition. During the conflict, the Baron Harkonnen is killed by Paul's younger sister, Alia. During negotiations, Paul kills Feyd-Rautha Harkonnen—jeez, tough negotiations—and effectively ends the Harkonnen line. Paul threatens to destroy the spice, so the Emperor gives in to the demands. Paul will marry the Emperor's daughter, Irulan. This secures Paul's right to the Imperium throne, and he basically becomes the most powerful man in the universe. And now, we've reached the end of the story.