Chapterhouse: Dune, written by Frank Herbert is the sixth and last novel in the original Dune series. It is also known variously as Chapterhouse Dune, Chapter House Dune and Chapter House: Dune.
The Bene Gesserit still find themselves questioning the Golden Path of humanity set by the God Emperor. Now they must survive the Honored Matres, whose reckless conquest of the Old Empire threatens [ene Gesserit survival. The Sisters must reassess their timeless methods: does ultimate survival go beyond calculated manipulation? Is there greater purpose to life than consolidating power?
Concluding the Dune saga
Chapterhouse: Dune ends on a cliffhanger with unanswered questions about the escaped ship, the merging of the Honored Matres and Bene Gesserit, the role of Scytale, the development of Idaho and Teg, what chased the Honored Matres, the role of the Jews, and the identity of the god-like characters in the book's final chapter.
Brian Herbert and Kevin J. Anderson have since worked on finishing two sequels to Chapterhouse: Dune which should answer all, or most of these question. The two volumes, named Hunters of Dune and Sandworms of Dune, are scheduled for release in 2006 and 2007 respectively.
There have been some hints in the prequel novels, written by Brian Herbert and Kevin J. Anderson, that the enemy that drove the Honored Matres back to the Old Empire was the remnants of the Thinking Machines. The Prelude books are based on notes by Frank Herbert and discussions Brian had with his father. In Dune: The Butlerian Jihad, an evermind overseeing Giedi Prime sends 5000 deep-space probes, equipped with copies of the evermind, as seeds for new Synchronized Worlds. Shortly thereafter, human forces arrive and retake the planet, destroying the evermind copy before it was backed-up, thus removing any and all knowledge of the probe/seeds. One of the probes lands on Arrakis and is promptly swallowed by a sandworm attracted by the vibrations caused by its internal factories. The fate of the other 4999 are unknown. It can be postulated that, due to the hazardous nature of deep space and the travel times projected by the evermind, i.e. hundreds to thousands of years, the probes may have suffered a significant failure and attrition rate.
In Dune: Battle of Corrin, the last evermind sends a copy of itself into deep space where it hopes to be able to rebuild the machine empire, and wait for the humans to arrive. It is unknown if the nascent Synchronized Worlds seeded by the probes intercept this broadcasted update. If they did, however, then the second machine empire would therefore be fully up to date on the course of the Butlerian Jihad. It is also stated by a Guildsman in House Corrino, when they are tossed into deep space, due to activation of shields while folding space, that they must get away fast because there is an "ancient and future enemy" approaching. This could be interpreted as the Thinking machines, the evermind copy sent to establish the "new" empire. They fit in as humanity's ancient enemy, since the Butlerian Jihad, and humanity's future enemy, possibly the one that drove the Honored Matres back.