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Act 1
All sunflowers in Green Hill Zone are pink instead of green. In the final game, only those seen in the ending sequence use this palette. The background is also laid out differently.
Giant balls are found across the three Acts. They move automatically to the left or right when the camera reaches a certain position, and exhibit some rudimentary physics as they move across the landscape, being capable of carrying its own momentum down hills and allowing it to move up half-pipes and hills. If a ball rolls off a ledge, it will jump into the air. However, the balls cannot recognise path swapper flags, and consequentially cannot make it through loops.
Sonic has no control over their speed or direction, though if the camera is far enough away, they will respawn. Should the balls collide with other objects (e.g. Badniks) nothing happens, however they are very capable of clipping through scenery or crushing Sonic depending on the situation. The balls can push Sonic around as it rolls, though this can also cause him to clip through the level collision in certain places. If he stands on top of a ball, it will react, but it will lose its ability to recognise level collision until he gets off of it.
The moving Newtrons have a different palette, being pink with yellow eyes instead of blue with red eyes.
The Newtrons that remain static and shoot also have a different palette, which is the blue colouring used by the moving Newtrons in the final.
All moving platforms move at the same speed, in unison. This makes it more difficult to get to the top path than in the final game.
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Act 2
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Act 3
Green Hill Zone is the only level to feature a boss. It's almost identical to the final game, but the lights on the chain do not flash, and Eggman does not laugh as the wrecking ball emerges.
Eggman does not laugh when he hits Sonic.
Beat him and his "burnt" animation does not show. His panic animation isn't drawn aren't after the fight, he just drifts away, switching between his shocked and normal expressions.
Like with signposts, Sonic does not immediately run to the right when the capsule is opened, and when the score tally appears, will punch the air if the player jumps. The animals emerge from the centre point and never face the camera.
There is also technically an "Act 4", which can be accessed by pressing 
on the level select. It's identical to Act 3 but has a strange title card and Sonic starts higher up.
You can run past Eggman in Act 4. Both lead to Marble Zone Act 1 once beaten.
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References
on the level select. It's identical to Act 3 but has a strange title card and Sonic starts higher up.
