My personal favorite 2D Metroid Game :D
User Rating: 10 | Metroid Fusion GBA
This game's awesome even if it is a 2D game it makes it up to create some great enviorments, boss battles and more as always you start as Samus Aran as your main character and the story plot takes place on SR388 where you are attacked by a strange lifeform called X this thing infects your nervous system and expands all over your body after crashing your ship in an asteroid they rescue you and take you to the HQ so they can examine whats wrong with you. They find out they can't take your suit cause it became integrated with your nervous systems so they create a Metroid based vaccine as a only hope with minimal success guaranteed. After being injected with it you miraculously survive and are sent to the Biologic Space Labs to investigate some recent incidents. Although the game just takes place on the BSL it's really cool cause it has some specific type areas like water, ice, etc as you play the game you'll recover some of your latent abilities as morph ball, super missiles etc. Really a game worth to play if you manage to find it at your local game store. 
