Basic twist for A:
The "superior being" is manipulating Michael and is actually the real bad guy, and the "evil emperor" was trying to warn Michael about them the whole time, he was sealed 1000 ago by the being (they can be siblings or something, and the 6 gems/6 islands can be some kind of symbol of their relationship). Maybe Michael is their son who can also use the power of the gems (I'm imagining two supreme rabbit parents lol)
Similar twist for B:
The "evil group" that collects for an "evil purpose" is only "evil" in Michael's eyes; He is the only bad one, while every one else is trying to keep him from obtaining the gems. The aforementioned group is an activist group that has tried to stop his reign of terror for generations, which would be carried on by collecting the gems (gems are like 6 of the 7 deadly sins, and Michael can be greed or something). Maybe the professor can be the one you feel bad for. They raised Michael and only wanted him to be happy, but being truly evil is what makes him happy?