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Automatically starts as Hyper Sonic when accessed via level select, unlike the final where you are Super Sonic if accessed in this way.
The background palette for The Doomsday Zone is the same as DEZ2's.
Various sound effects are still missing.
The zone scrolls a lot more slowly to begin with. You can speed up the scrolling by holding Right to gradually accelerate it, but hitting an asteroid will slow it down again.
There are a lot more asteroids at the start and a lot more missiles before reaching Eggman.
There are still lots of rings before reaching Eggman, as there are still no rings during the final chase.
When the boss reappears after its blue armour is destroyed the 'badnik popped' sound effect plays instead of the sound played in the final.
The latter half of Doomsday has no rings and asteroids and the projectiles Eggman fires have different graphics, especially the underneath weaponry.
When you hit Robotnik while chasing him, you don't get knocked back like you do in the final.
When The Doomsday Zone is cleared, the game goes back to the Level Select.