Plotlines
During the events of Dune, the Padishah Emperor Shaddam Corrino IV grants Duke Leto Atreides I control of the lucrative spice harvesting operations of Arrakis, ousting the Atreides' longtime rivals, the Harkonnens. The Atreides rule is cut short by a murderous conspiracy crafted by the Harkonnens and Emperor himself. Leto's son Paul Atreides (known by the Fremen as Muad'Dib) later leads a massive Fremen army to victory over the Emperor's Sardaukar soldier-fanatics, and by threatening the destruction of all spice production on Arrakis manages to depose Shaddam and ascend the throne in his place. With Emperor Paul worshipped as a god, Arrakis becomes the governmental and religious center of the Imperium.
Paul Muad'Dib continues the efforts to terraform Arrakis into a green world, a plan begun by the Fremen under the guidance of Imperial Planetologist Pardot Kynes and his son Liet-Kynes. The core of their plan is gradual water-collection from the Arrakeen atmosphere to form large reservoirs that would, eventually, become lakes and oceans. Much of this activity takes place in the unexplored southern latitudes of Arrakis.
By the time of Children of Dune, Alia Atreides (and then Leto II and Ghanima) realize that the ecological transformation of Arrakis is altering the sandworm cycle, which would eventually result in the end of all spice production. This at first seems a future to be avoided, but Leto II later uses this eventuality as part of his Golden Path to ultimately save humanity. Once he himself begins the transformation into a human/sandworm hybrid, he eradicates all desert on Arrakis except for a small area he makes his base of operations, and destroys all of the sandworms save one — himself.
After his death some 3,500 years later in God Emperor of Dune, Leto's worm-body is transformed back into sandtrout. Within only a few centuries, these sandtrout return Arrakis (thence called 'Rakis') to a desert.
In Heretics of Dune, all life on Arrakis is destroyed (and the entire surface of the planet slagged into oblivion) by the Honored Matres in a failed attempt to eliminate the latest Duncan Idaho ghola. The Bene Gesserit escape with a single sandworm, and drown it to revert the worm back into sandtrout. In Chapterhouse: Dune the Bene Gesserit use these sandtrout to begin a new sandworm cycle on their homeworld of Chapterhouse, which is terraformed into desert for this purpose.
Finally, in Sandworms of Dune, some sandworms are revealed to be alive and well, having sensed the upper crust would be destroyed, and therefore burrowed even deeper, escaping the blast.
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