For twenty-six years, the Ithaca wandered uncharted space fleeing numerous times from the tachyon net cast by the mysterious figures of Daniel and Marty, who were revealed to be Omnius and Erasmus. Also during their travels, the crew discovered the world of the Handlers, in which some of the crew members were replaced with Enhanced Face Dancers in service of their leader, and servant of the Machine leaders, the Face Dancer himself, Khrone.
After several years, and in a effort to equip them with the necessary weapons to defeat the Enemy chasing them, the crew created Gholas of famous heros/villians from Dune's past. Some of the gholas were Paul Atreides, Jessica Atreides, Chani, Stilgar, Liet Kynes, Leto Atreides II, and Dr. Wellington Yueh.
Eventually, with the assistance of The Oracle of Time, the Ithaca returned to the Known Universe and crashes on the stronghold of the Thinking Machines, who have returned to finish the war against humanity in the climatic Kralizec battle.