The Sandopolis Zone is a large desert area with ancient pyramids which mark a bygone civilization. The Zone is also filled with many ruins and old buildings which Knuckles is determined to preserve. The focal point of the Sandopolis Zone is the Lost Pyramid of Sandopolis, a giant pyramid which used to be submerged in the sand dunes. In front of its entrance is a large pool of quicksand.
Sonic and Knuckles met each other in the Sandopolis Zone while they were independently traveling to the Launch Base Zone (conflated with the Lava Reef Zone here, as it is on a volcano) to prevent the launch of the Death Egg II. However, they were sidetracked by the sudden appearance of Captain Plunder, who had traveled to the island with his Sky Pirates to loot the treasure of the Lost Pyramid of Sandopolis (much to Knuckles' consternation). Along with his assistants Filch and the Professor, he managed to raise the pyramid out of the ground.
A Stone Guardian appeared from the pyramid, claiming that all heretics must die. Knuckles and Sonic defeated it by luring it into a quicksand pit, only for the pirates to sneak into the pyramid while they were occupied. The pirates activated an ancient lighting system and loaded up on treasure from the tomb, but fled for the exit as soon as the lights went out. Knuckles was happy to let them go, since he knew about the pyramid's curse. Sure enough, the pirates were soon attacked by three Hyudoros and were forced to drop their treasure in order to escape.
Still in the pyramid's central tomb, Knuckles broke an ancient seal on the wall, allowing sand to flow into the pyramid, burying it again. Before they were buried themselves, Knuckles used his knowledge of the ancient texts to lead Sonic into a secret tunnel through which they escaped.
The Pyramid was later unearthed once again by Nack the Weasel, who found it by shrinking the sand with his shrinking technology. Once inside, Nack discovered yet another Stone Guardian, dedicated to protecting the treasure chamber. By unknown means, he was able to reprogram the guardian to work for him. When Knuckles and Chaotix followed Nack to the Pyramid, they had to fight both the guardian and the pyramid's ghosts. Nevertheless, Nack was able to escape the Pyramid, shrinking down all of the treasure so that he could carry it away in a single box, then enlarge it later before selling it on. Outside the Pyramid, Knuckles was able to stop Nack from leaving the Island by using Nack's shrink ray to re-enlarge all of the treasure, exploding Nack's plane from within. Nack was captured, but Chaotix left the scene leaving Knuckles to pick up all the treasure, which had been scattered across the desert.