So I sent my plot idea to Huck, and he accepted it, so I'm posting it here as well.
Majora's magic is still in effect on Skull Kid, it's giving off a poisonous aura, which effects those around him, and that's what turns them into ReDeads as mentioned in the SU area. So Link must work together with some of the other characters to break the curse. So Skull kid isn't evil, but Majora's poison is reeking off of him into the people around him. Link and skull kid are immune, and some of the others, Zant, Solro, and possibly some of the others, if you have a reason why. Like, Zelda may be immune because of the mystical power that runs through the royal princesses blood.
Anyone else think this sounds like a good idea?