It should be Metroid: Zero Mission (Game Boy Advance) / Metroid (NES). They are the same game (Zero Mission is just a remake, but it adds a little bit at the end of the game after you beat Mother Brain).
That wasn't a Mother Brain in Metroid Prime 3: Corruption, it was a Aurora Unit (which looks similar to Mother Brain's. Mother Brain was created by the Chozo before turning on them to join the Space Pirates, Aurora Units were created by the Federation).