This is what the story behind the song is:.
Mary: She is pretty, popular and talented but she gives guys the wrong impression and ends up pregnant (possibly the white kids child, but it ruins her chances of fame).
White boy: Badly bullied for being a geek. Though he has a lot of knowledge, nobody sees it as a good thing. His father is abusing his mother, and one day he can't take anymore, so he kills himself.
Greg: Great at basketball and could've been very successful and famous. He had a lot of talent, and someone was jealous of him, so they murdered him.
The message that the song is giving really is: people with a lot of talent, aren't apreciated as well as they should be!