WOW!!! You must really Sonic that bad, huh?
I don't care if Sonic or Mario die, either way, they're both my favorite characters. Anyway, lemmie give ya some ideas for your sequal:
1. Luigi talks Mario and tells him that it's too dangerous for him to do his mission and Luigi would die of honor wiping out the clone army himself.
2. Luigi turns traitorous to him and works with the Sonic clone army, Mario survives when he's revived from a 1-up mushroom from Peach and start a new adventure to see who's behind all this.
3. Mario realises that Luigi made the army to take over the world and get revenge on Mario for using him. LOL! That's from Luigi's Revenge also. It would be the sequal and Mario's alive again.
OR
4. Mario relises that not only there's a Sonic Clone army but a Luigi Clone army too, and must rescue the REAL Luigi and Sonic that are trapped in the clonning glass containers from the cloning machine, along with other characters such as Tails, or Peach. And Dr. Eggman, or Robotnik, or whatever his name is, is behind all this to grab the chaos emeralds to... well, ya know the rest.
So there you have it. Four really big Ideas for your sequal that I can come up with. Good Luck Choosing.
BTW what techno song is that on the Preloader page?