For three years, the
no-ship Ithaca has been in an alternate universe, hiding from the "great enemy". It carries the clones, or
gholas, of
Duncan Idaho and famous military commander
Miles Teg; plus the
Bene Gesserit Sheeana, the last
Bene Tleilax Master
Scytale, a group of
Jews, other humans, four Futar man-beasts, and seven small
melange-producing sandworms. Scytale has shared the secret of producing melange, also called "spice", in tanks, because the sandworms do not produce enough to allow the ship to continue traveling. The mysterious
Oracle of Time speaks to Duncan and brings the no-ship back into the "regular" universe. The ship is discovered by the mysterious
Daniel and Marty, mentioned at the end of
Chapterhouse: Dune. They attempt to capture the ship, but it escapes. On Chapterhouse, the only remaining source of spice,
Murbella, now the leader of the Honored Matres and Bene Gesserit, attempts to merge the groups into the New Sisterhood and prevent civil war, despite the ultimately-fatal bickering of Bene Gesserit Bellonda and Honored Matre Doria. Desperate for more spice so that their
Navigators can travel through space, the
Spacing Guild approaches her, but Murbella refuses, threatening to cut them off completely. Known only to the Bene Gesserit, the Chapterhouse sandworms produce little melange; the Bene Gesserit make up the shortfall with their own stockpiles. Though Honored Matres destroyed nearly all Bene Tleilax worlds, their descendants (the
Lost Tleilaxu) have returned from
the Scattering. They use the shape-stealing
Face Dancers for espionage, until the Face Dancers kill Tleilaxu Elder
Burah and replace him with a duplicate. It is revealed that they replaced all Lost Tleilaxu Elders, as well as countless humans on various
Old Empire planets. Their leader
Khrone sends Tleilaxu scribe
Uxtal to serve rebel Honored Matre leader
Hellica, who proclaimed herself
Matre Superior and now rules the conquered Bene Tleilax homeworld,
Tleilax. The desperate Spacing Guild goes to
Ix seeking an alternative means of space travel. Khrone and his Face Dancers secretly infiltrated Ix, plotting to dominate the universe. Working with Daniel and Marty, Khrone offers their advanced navigation technology to the Guild as if it were Ixian-designed. The Guild agrees to develop this technology if they have a
monopoly on it. Uxtal is forced to use Tleilaxu
axlotl tank technology to produce the
adrenaline-enhancing drug Honored Matres use. Khrone tasks Uxtal to make a ghola of Baron
Vladimir Harkonnen as
sociopathic as the original. Khrone obtains the blood of
Paul Atreides and has Uxtal make a ghola of Paul; he intends to use the Baron's ghola to twist Paul's ghola into a weapon for Daniel and Marty's conquest of the universe. Later, Guild Navigator
Edrik comes to Tleilax seeking Uxtal's knowledge of axlotl tanks; the Navigator fears his kind's obsolescence when Ixian navigation technology becomes available. He seeks a tank-based source of spice to break the Bene Gesserit monopoly, but everyone believes that technology died with the Tleilaxu Masters. Eventually, Uxtal accesses the genetic material of deceased Master
Waff, and creates several Waff gholas, hoping to recover the technology. The Tleilaxu sustain their lives indefinitely using gholas; Scytale's current body is dying, and he lacks a replacement. He has a secret to use as a bargaining tool: a hidden
nullentropy capsule containing cells of numerous important historical figures secretly collected by Tleilaxu for millennia, as far back as the
Butlerian Jihad. The Bene Gesserit viciously debate over whether to create gholas of any of them. A few at a time, the historical gholas are created, and Scytale is given a new body. On Chapterhouse, Murbella creates the Valkyries, an elite New Sisterhood strike force. They successfully attack rebel Honored Matre strongholds on other planets, discovering that some Matres are disguised Face Dancers. Murbella accesses
Other Memory from her Matre ancestors and learns their true origins: they were vengeful Tleilaxu females, freed and assimilated by
Fish Speakers and Bene Gesserit fleeing in the Scattering. Tleilaxu females had been enslaved for use as axlotl tanks by Tleilaxu males for millennia. These origins were forgotten; Murbella now understands why Honored Matres annihilated Tleilaxu worlds in the Old Empire. On the no-ship, rebel Bene Gesserit attempt to murder the Leto II ghola, but are foiled when he transforms into a sandworm. Sheeana has visions that suggest the use of the gholas is dangerous, and halts the program until she knows more. The Paul ghola, helped by the Chani ghola, steals and consumes an overdose of spice in an attempt to remember his past, but instead has a vision of being stabbed by an evil version of himself. After the Bene Gesserit discover him, he concludes he has regained
prescience. Daniel and Marty tell Khrone to discard the Baron and Paul gholas, as they have lured the
Ithaca into a trap, and expect soon to capture the Paul ghola. Working to his own ends, Khrone continues to prepare the gholas, restoring the Baron's memories - including Alia, who taunts the Baron - and instructing him to train the Paul ghola, which he renames
Paolo. Paolo does not yet have his memories. Murbella contracts Ix's competitor
Richese to provide armaments to fight the great enemy, but rebel Honored Matres destroy the planet to cripple the Sisterhood. Murbella and her Valkyries - including her daughter Janess Idaho - successfully assault Tleilax, the most powerful rebel Matre stronghold, and discover that many, including Matre Superior Hellica, were Face Dancers. Uxtal, after suffering forced sexual imprinting by ugly crone Matre Ingva, dies trying to escape, eaten by sligs, but the only surviving Waff ghola finds refuge with the Spacing Guild, offering Edrik genetic knowledge for the Guild to create their own sandworms. The
Ithaca stumbles upon the homeworld of the Futars'
Handlers. An exploratory party discovers that the "Handlers" are actually Face Dancers, and barely escape back to the ship, aided by the self-sacrifice of Hrrm the Futar. Some Face Dancer ships crash into the
Ithaca, and the chaos makes it impossible to know if Face Dancers replaced any passengers. The emergency forces Teg to reveal his hidden power of superhuman speed. Duncan, who considers making a Murbella ghola, is cured of his Murbella obsession by mutual imprinting with Sheanna. Murbella, now in complete control of Honored Matres and Bene Gesserit, prepares a defense against the great enemy, now identified by Other Memory to be
thinking machines of
Omnius, the machine overlord destroyed in the ancient Butlerian Jihad. The
Oracle of Time is revealed to be the living consciousness of
Norma Cenva, somehow also still in existence millennia after the Jihad. Daniel and Marty are revealed to be Omnius and the independent robot,
Erasmus. Before its destruction, the Omnius incarnation on
Giedi Prime had launched thousands of probes capable of constructing new machine colonies on any planets encountered. One probe eventually intercepted a signal transmitted by the last remaining Omnius on
Corrin before it too was destroyed. Its forces and Synchronized Empire finally reassembled, the new version of the Evermind is on the way back to the Old Empire to destroy all humanity. ==Reception==