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How to beat the last boss easily
As Sonic and Knuckles go to the final stage and when you get to the Egg Man boss you have to jump and press up and A at the same time when he doesn't have anything guarding his head. You may get hit one or two times and you will need to hit the boss 6 or 7 times before he is defeated.
submitted by: Tom

Change color settings
Press R at the "Press Start" screen. In the upper right corner, the game will display the color setting that you are currently on. Press R again to change the color settings. There are three color setting: "Game Boy Advance", "Game Boy Advance SP", and "Game Boy Player". The color settings optimize the color for the system that you are using.

Secret Stage mode
After complete all seven special stages, return to the main menu and press Up, L, Down, R, Right, Left.

Play as Knuckles
In a new game, complete all three Acts of Sunset Hill Zone with Sonic as the leader.

Play as Amy
In a new game, complete all three Acts of Toy Kingdom Zone with Sonic as the leader.

Play as Cream
In a new game, complete all three Acts of Cyber Track Zone with Sonic as the leader.

Sound test
Successfully complete the game. You do not need all the Chaos Emeralds. The "Sound Test" option will appear just above "Delete Game Data" in the options menu.

Eggman as partner
After collecting all the Emeralds, play the "Final Boss level" with Sonic as the leader and anyone else as your partner. Once you change to Super Sonic, Dr. Eggman will become your partner in order to help you defeat the final Boss.

Easy height
Have Tails as your partner. If you missed an elevated platform or area during a level, use Tails' Tag action on the ground. About 95% of the time you will be able to reach what you fell off from. Note: This can also be done to access certain areas of the Act faster.

Moonwalk
Your character can run backwards by holding [R] and preparing the Tag Action (do not use it). Run and jump in the air. When in the air, press the D-Pad in the opposite direction you are running and do not touch it afterwards. Your character will run in a direction and he or she will be facing the other way. This is best done as Sonic, as he is the fastest character.

Sonic The Hedgehog reference
In Zone 2, Sunset Hill, the music that plays is a remix of Green Hill Zone from Sonic The Hedgehog.