Metroid Fusion. The game that trades quantity for quality.
This story is the last in the current timeline. It begins with Samus escorting Federation troopers onto SR388. She is then attacked by a mysterious life form known as the X. The X multiply inside her and leave her unconcious, corrupting parts of her Power Suit. Just before her ship spins out of control into an asteroid belt she is jettisoned from the ship and picked up by the Federation, who surgically remove parts of her Power Suit, dramatically altering her physical appearance. However, Samus herself was still corrupted by the X. She was given a survival chance of under 1%. Then somebody found a cure. A Metroid vaccine created from a cell of the last infant metroid was administered and the X were completely destroyed.
It is Samus' job to eneter the BSL research lab and stop the X, or die trying.
I give this game a rating of 9/10, the only reason I cannot class it as perfect is the shortness of the game.