Ummm... Is Mario really a good guy?

[Kriven]

That just sounds like theory. I've played the game more times than I can count and I can tell you that definitely did not come up in the game at all. And from what I can tell, the paintbrush is what actually gives him the ability to take on the Shadow Mario form. That is the reason that the Shadow Mario form is vulnerable to FLUDD's water.

Shadow Mario comes from Jr's mask, evidenced by the crudely drawn Mario face on it and how he always puts it on to transform.