I personally think that the "person" behind all of the murders is Master Hand, turning all his kills into trophies (stuffing them and leaving their intestines...) I've thought this for a while, and before Bowser died he said something like "He'll be back, he has a prize to collect"
*Lightbulb* Oh Mama Mia, it all makes perfect sense. He can appear out of nowhere, has a personal arsenal of finger missles & lasers, and he can fly.
Master Hand is the Master Mind to this entire plan.
Master Hand commands the army of Mr.Game&Watch. He manipulated Ganondorf with promises of ruling the Mushroom Kingdom. Ganondorf then manipulated Zelda with false promises of power. Ganondorf used Olimar the Spaceman to create the explosive pills. Ganondorf said they would be used to "take care of the competition" and he used one to blow up Red's house. Why? Simple, because Red's a Pokemon Trainer and a Pokemon trainer basically commands powerful monsters. Red collected so many Pokemon that they would have been helpful to fight the army of MR.G&W's. Master Hand wanted to crush any possible threats.
Master Hand will be the one to truly control the Mushroom Kingdom. Ganondorf and Zelda don't know they are nothing but puppets; Master Hand is
literally the HAND pulling the strings!
.....Mama Mia.