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Back in the day, I read the first 2 1/2 or so Dune books and I'm wondering who ends up ruling the universe at the end of the series. I know there was a Sandworm Atreides emperor who ruled for a few millennia and then he committed suicide due to galactic stagnation.
So as far as Frank Herbert was concerned, rather than his son, who rules the universe at the end of the Dune saga?
At the end of Chapterhouse: Dune, the last REAL Dune book by Frank Herbert, no one "rules the universe", or even the galaxy.
The Honored Matre-turned-Bene Gesserit Murbella has become the head of both groups of women, and the Duncan Idaho ghola has escaped with Sheeana and others on the no-ship kept on Chapterhouse Planet. Whether the Old Empire will be overrun by whatever Enemy the Honored Matres were fleeing is an open question.
The whole point of Leto II's Golden Path was to free humankind from the possibility of ever again being controlled by one person or organization and from the danger of being wiped out by a single natural or artificial disaster.
No one rules the Duniverse at the end.
The swordmaster, Duncan Idaho, the Ghola is engineered to be a superior mentat, and is designed to do full galaxy wide super long range planning for humanity. I vaguley remember the ghola's rule for 40 or 60k years.
No named character rules the Universe at the end of the Dune saga. There is a vast interstellar empire in Dune which rules thousands or millions of star systems.
But there are hundreds of billions of stars in our galaxy and hundreds of billions of galaxies in the observed part of the universe. Thus the Human space empire in Dune rules a tiny drop in the sea of space.
And the mightiest alien space emperor who might exist in the Dune universe unknown to the characters and the readers does not rule the universe, because he does not rule the Human Empire.
If the empire in Dune ruled the Universe, the highest nobles in Dune would not be dukes. There would be kings ruling kingdoms, subordinate to Kings of kings (kings to the second power) who would be subordinate to kings of kings of kings (kings to the third power) and on up to kings to the 47th power, kings to the 99th power, kings to the 457th power, kings to the 1,826th power and on up to THE EMPEROR.
Answer -- nobody!
That's a big part of Leto II provoking the Scattering. He wanted the human race to scatter so far and wide that no one nation, no one power -- not even prescience -- could trap them all into the same future. In Chapterhouse, I believe someone estimates the population of the Scattering as "megatrillions".
That said, clearly the local neighborhood has a big dog, that being the Face Dancers. We get hints that there are multiple factions out there whose attitude toward the Honored Matres was "Get Them!" But the ex-Tleilaxu Face Dancers were the ones who kicked their butts and confiscated almost all of their secret weapon. Those facts hint that at least in the local region, the FD's are the tops.
Hmm ... a problem just occurred to me... Okay, we note that the BGs have essentially taken over the HMs by surrendering to them. Nice gambit, but there's a problem. Remember all those "Get Them" guys out there in the Scattering? They hate the HMs with a burning passion. They might not buy the notion "Oh, we're a lot nicer now that we had a corporate merger with the Bene Gesserit". I think the BG/HM combination has inherited a lot of powerful enemies!
[SPOILER-ALERT]tag!