For twenty years, the Ithaca wanders uncharted space fleeing from the net cast by the mysterious figures of Daniel and Marty. Also during their travels, the crew discover the world of the Handlers in which some members are replaced with Face Dancers in service of Khrone. After several years and in a effort to equip them with the necessary weapons to defeat the enemy chasing them, the crew creates Gholas of famous heros/villians from Dune's past. The gholas are 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 returns 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.