Mystery of the Sandopolis Zone is a 2-part Sonic the Hedgehog beginning in Issue 47 of Sonic the Comic. It continued the Sonic 3 & Knuckles story arc, this time with the Sonic & Knuckles series of events.
Once again, Sonic the Hedgehog and Tails have returned to the Floating Island on the bi-plane. Upon spotting it, Sonic leaps off the plane, Tails wishing he could join him. Sonic lands in the Sandopolis Zone; Porker Lewis has advised him that he'll be able to get a good view of the Death Egg behind some ruins and, sure enough, Sonic spots the battleship being repaired in the Launch Base Zone. Before Sonic can think too much about stopping Doctor Robotnik, the ground begins to shake and a Sandworm leaps out of the sand to attack. The Badnik slams into Sonic twice before disappearing back underground. Knuckles the Echidna takes this opportunity to appear, asking Sonic what he's doing here again. Knuckles offers to help but Sonic rebukes him, just as the Sandworm leaps out from behind him again. This time Sonic's prepared and he launches a backwards Spin Attack, trashing his enemy. Sonic reveals he is on his way to the Death Egg, something that Knuckles was also doing before his adventure with the Marxio Brothers. Sonic is about to warn Knuckles off the dangerous feat ahead of him before the pair are interrupted by Captain Plunder.
Plunder reveals he is here for treasure, something Knuckles doesn't take too kindly. The nefarious pirate simply pats Knuckles on the head and orders The Per'fessor to get on with work. Sonic asks who the professor is, Plunder replying that he's from Metropolis Zone's university. Soon enough, the professor has decoded some ancient symbols and prised open the door of an ancient building. Inside, he presses a button and, soon, the whole area begins to shake. Knuckles is livid, holding Plunder responsible if any of the old buildings are damaged. The plan soon unfolds as a pyramid emerges from the ground, taking Sonic with it as it rises towards the sky. Ecstatic that his plan has worked, Plunder introduces everyone to the Lost Pyramid of Sandopolis.
The outlook soon changes as a giant Stone Guardian appears from the pyramid's door. Plunder reveals that his map had mentioned some "nonsense" about a guardian, but he had paid it no heed. The guardian speaks, condemning anyone who summoned the pyramid to death. Sonic launches a spin attack and shatters the guardian immediately, but Knuckles warns Sonic to look behind him - the guardian is rebuilding itself! Sonic isn't having any of it, but he comes to his senses as the guardian punches him into the ground. Knuckles steps onto a boulder and taunts the guardian, having read the sacred text. The guardian follows but soon finds itself in a pool of quicksand, part of Knuckles' plan all along. As the opponent sinks beyond trace, Sonic berates Knuckles for losing Plunder. He also asks why the guardian attacked Knuckles if he was the master of the island. Further into the pyramid, Plunder turns on a light which reveals a room filled with treasure. As Plunder and The Per'fessor fill bags (Filch can't, he's a ghost, see?), Knuckles finds them and warns them against the theft.
Just then, the lights go out and Plunder and his team make a break for it. Sonic gets ready to give chase, but Knuckles stops him. When the lights go out, a curse is said to activate. Sure enough, small glowing objects seem to be following the thieves. Filch sees them and alerts Plunder, who shouts his lieutenant down. Filch eventually gets his captain to turn around, the three of them terrified by three fully-formed ghosts. Since these are the "wrong sort of ghosts", Filch abandons any hope of negotiation and the three pirates flee, just managing to get out of the pyramid before the door closes behind them. Unfortunately, none of them have made it outside with any treasure, dropping their sacks on the way out. Inside, Knuckles finds a seal and breaks it, causing sand to flood in from outside. Since this will eventually sink the pyramid underground permanently, the heroes slip out a secret exit. On Plunder's ship, Filch recounts their adventure to the rest of the Sky Pirates, perhaps exaggerating slightly...
- This story starts the Sonic & Knuckles adaptation, although the Sonic 3 & Knuckles story arc had never really stopped, the previous part having anything to do with the story being Day of the Death Egg.
- Plunder's appearance in this story ran concurrently with Captain Plunder & His Sky Pirates!, although the Plunder solo story was said to occur before the Sonic story.
- The Per'fessor never appeared again, nor did the Sandopolis Zone, at least not in Sonic the Comic. It did however reappear in Traitor of the Lost Pyramid in the Knuckles Knock-Out Special.