Just remembered it when reading nite's topic. Here's how it goes.
The first level is bowser's castle. You basically go through it like a normal bowser's castle, save for the fact that luigi is close behind you. When you reach bowser, luigi gets shut outside. You fight bowser like you normally would, and when he's nearly defeated, he whips out some weird potion and drinks it. When you approach him, he shoots a giant blue flame, and the screen goes black.
Acinema of close up on mario's face. He's coming too. Then, it zooms out, and mario looks completely different, sort of megaman-x ish. Then e-gadd comes in. Or, actually, his son. He tells you that bowser somehow froze you, and luigi actually defeated him. Mario sayed frozen until this time in the future, when one of e-gadd's sons figured out how to bring mario's brain back to life in a robot.
You go walking around the old mushroom kingdom, which is for some reason in rubble. On your way, you get attacked by various big tanks and such. You go in, and the rubble is nearly deserted. You find some old tapes, and discover how luigi was rewarded for defeating bowser once and for all, how, because bowser was gone away, luigi and peach got married, and how after they died bowser's son (grown-up bowser jr) lead an army and devistated the mushroom kingdom.
Now realizing your fate, you eventually run into Princess Mario, aka luigi and princess peach's daughter. She is the leader of the mushroom resistance squad. You help them out in various areas, getting upgrades to your body (I'm a big MMX fan, early games 1-3) and such. You sometimes run into what appears to be wario in a cloak, who Spoilers:
| happens to be a robot controlled by the spirit of Geno, OMG, and |
gives you advice and useful tips which help you pass through the game.
Eventually you run into what appears to be a robot luigi, but is actually bowser's brain in a robot, made by e-vil, the "bad" son of e-gadd. You defeat them both and restore peace. Happy end.
Old idea, but it flushed up so I wiped it onto a topic. Maybe it will be useful to a gamer with writer's block.
Dr. Wario