The Prophet was a term used by the Tleilaxu to describe the one, or man, who came to the universe to show the pathway to God. The Tleilaxu also believed that the Prophet's home was Rakis, and that he belonged and flourished there.
A tenet of the Great Belief, the Tleilaxu believed that the latest incarnation of the Prophet was the God Emperor Leto Atreides II. Even after his subsequent assassination by Nayla, and the dispersal of his Sandtrout in Rakis, only served to enhance this vision among the gnome-like men. After The Scattering, and during the Return of the Honored Matres, the Tleilaxu continued to believe that the Sandworms on Dune, contained the pearl of essence of the God Emperor. When the Matres destroyed Rakis, and killed all of the worms, many Tleilaxu believed that the Prophet would never return to his home.
Later, during the time of the advent of Kralizec, the reborn ghola of Tylwyth Waff, a Tleilaxu Master made it his life's mission to restore the Prophet to the sands of Dune. Waff bargained with Edrik, a Guild Navigator, that he could genetically create for the Steersman, a worm that would be their own monopolized source of melange. In return, Edrik would have to give to Waff, a few sandworm specimens to experiment as he saw fit.
Waff fulfilled his promise to the Guild, and produced Seaworms, which produced a super-potent version of spice, called Ultraspice. The second set of worms, Waff intended to return to the sands of Dune; after he enhanced their armor-piercing ability through genetic engineering, which he did.
All through this process, Waff considered it his holy duty to God, to return the essence of the Prophet to the sands of Dune. As the day of Kralizec happened, and the final battle between man and machines were occurring over Chapterhouse and Junction; Waff was pre-occupied and released his improved sandworms into Rakis. As the leaders of humanity, and the leaders of the Thinking Machines, were dueling to the death on Synchrony; Waff was monitoring his released worms under the Dune surface.
Waff became despondent when all of his enhanced worms died on Rakis just a short time later. But to Waff's great joy, Waff soon found that deep under Rakis's surface; sandworms containing the essence of the Prophet, Leto Atreides II, were alive, and had been for over 40 years! As the giant worms bounded to the surface, and cut through the fused fused-glass surface of the planet, Waff allowed one of the giant worms to engulf him, and eat him—becoming one with his Prophet.