Restore Health and Firing Over Ledges
While Metroid Fusion does not have a place where you can input codes for cheats, there are several techniques that you can use that are either secret or a programming glitch. Two such codes exist: a way to restore Samus' health and a way to fire a weapon while you are hanging onto a ledge, thereby remaining in cover.
To restore Samus' health, quickly press and hold the down on the Game Boy's directional pad and simultaneously press the "B" button. If done properly, Samus' health should restore.
If you want to fire a weapon while you are hanging onto a ledge, you need to have the wide beam. While hanging on the ledge, hold down the attack button to charge your wide beam and then release the button when the beam is fully charged. This will enable you to fire a weapon from pseudo-cover.
Secret Message
To unlock a secret message involving Samus, Adam, and the Secret Guy, you must first defeat Nightmare in Sector 5. Defeat Nightmare by shooting at the circle that appears underneath Nightmare when Nightmare is above you. Once Nightmare begins to fire only two lasers, switch your weapon to the Charge Beam and repeat the process. Once Nightmare is defeated, return to a Navigation Room; be sure that you do not pick up the Diffusion Missile upgrade. Once in the Navigation Room, a secret message will play.
Changing Samus' Appearance at the End of the Game
Metroid Fusion has several alternate endings; basically, the ending changes what Samus looks like. To achieve the "best" ending--with Samus out of her suit and in side profile--beat the game in under two hours with a 100% completion. If you beat the game in under two hours, but do not achieve a 100% completion, you see Samus without her suit leaning against a wall. Beating the game over two hours with a 100% completion rate shows you Samus without a suit in a city. Lastly, beating the game under four hours and under 100% completion simply shows you Samus with her helmet off.