This one is pretty easy to follow the rules on, but extremely difficult to accomplish. Set the game to the hardest difficulty possible, and then collect only the upgrades required by the game: No extra energy tanks, no extra missiles, except what you are forced to pick up. Given how absurdly hard these games can be on hypermode, you had better be pretty good at the Metroid Prime Trilogy or expect to fail. I know, because when I beat Metroid Prime 1 on hypermode, it took me about 10 tries to beat Meta Ridley with all energy tank and missile upgrades available.
I could just be really bad at the game. Or, it could actually be difficult already. But why not make it even harder?