Nice pixel-art piece. The mostly two-tone makes the fireball stand out, but you manage enough contrast with only the black and olive-green to give the scene real depth and a sense of overall scale. The Metroid inspiration is there and it is clear once you've seen it, but still it isn't obvious at first.
I think you've captured the essence and the humanity of the Samus/Mother Brain battle (which is really a David-and-Goliath struggle), still putting it in a sci-fi venue, and managed not to duplicate the Metroid scene. That's really good art, portraying exactly the conflict you wanted. Keep it up.