Cloud of Darkness just kindof was like... "hay gais I'm laik the final boss surprise surprise PARTICLE BEAM!"
Xande actually had a more in-depth backstory about hating his actual truly amazing gift that he couldn't comprehend. (SPOILER)mortality
I would go more in depth about it but I haven't played that game in ages so I don't remember most of it. I'll let someone do an essay length comment on it later.

In my opinion Xande was the main villain.