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The Special Stages for the Super Emeralds are completely different from Sonic & Knuckles. The colors are exactly the same as the Special Stages of Sonic the Hedgehog 3, but the sphere arrangements are completely different. Some of the layouts would become different Special Stages, and some would be outright dropped altogether. For example, the planned third Special Stage in this build became the hidden eighth in Sonic & Knuckles.
Special Stage 1
This layout is a completely different layout that was later scrapped. There are no Rings, so it's impossible to get a Perfect Bonus in this layout.
Special Stage 2
This layout is a completely different layout that was later scrapped.
Special Stage 3
This layout would become the hidden eighth Special Stage in Sonic & Knuckles. The only difference is that the 4x4 sphere grids in the corners are all blue.
Special Stage 4
This layout would remain in place as the fourth Special Stage in Sonic & Knuckles, but with some changes. The first ring of blue spheres has some extra blue spheres (with a blue sphere being directly beneath where the player starts), the path leading from the fourth ring of spheres has no blue spheres or bumpers, and the end of the Special Stage has only one blue sphere for the player to land on instead of two that the player will bounce backwards into.
Special Stage 5
This layout would remain in place as the fifth Special Stage in Sonic & Knuckles, but with some changes. The space the player starts out in is slightly bigger, and there are more blue spheres to collect.
Special Stage 6
This layout would become the third Special Stage in Sonic & Knuckles, but with some changes. The layout as a whole feels more open compared to the final, with some of the 3x3 grids facing outwards rather than all of them facing outwards. The player also has a different starting position.
Special Stage 7
This layout is an exact copy of the seventh Special Stage of Sonic 3. It might have been just a carryover given the nature of development both games share.
Special Stage 8
This layout is an early version of what would become the seventh Special Stage in Sonic & Knuckles. The player starts in a narrow corridor of red spheres instead of an enclosed space with two 3x3 blue sphere clusters, and the three bigger sphere grids are all different.