As with other stages in this game, Rusty Ruin consists of two standard Acts followed by a third Act containing only the boss fight. In Acts 1 and 2, Sonic must free captured Flickies from inside badniks, depositing five of the birds into a Goal Ring to progress between sections of the level (usually three per Act).
Rusty Ruin looks as though it's been beneath the waves until quite recently, what with all the soggy kelp-grass littering the stonework. Robotnik has presumably dredged the place out of the sea in his search for the Chaos Emeralds, and repaired the old traps of another of Earths' long-dead civilizations. Swinging iron maces and flamethrower traps abound. Geographically, the zone is located on Flickies' Island.
Rows of fans set in the floor enable Sonic to perform a Whirl Attack—a kind of spinning pirouette which bears remarkably similarities to Espio's maneuver in Knuckles' Chaotix. While spinning like this, Sonic can break down otherwise impenetrable pillar obstacles, although his handling becomes much more difficult to control.
- Main Article: Eggmobile (armored)
Reviving a tactic he last used in Sonic 3 & Knuckles's Sandopolis Zone, the ever-despicable Eggman locks his Egg-O-Matic onto a giant suit of ancient armor and attempts to crush Sonic with stone claws. A cannon attached to the base, periodically spewing shots across the arena, doesn't help matters either. To defeat Eggman, Sonic must leap atop the hands when they smash to the ground, and then ride them up higher to get in range of the Doctor's pod.
- In the beginning of the stage, there is a hole that presumably looks like what Sonic used to come in from. However, using the Spin Dash reveals a hidden 1-up inside it.