This movie is a high school satire done absolutely amazingly. It's everything current high school dramas wish they were. It's dark, funny, but does not lose any of its meaning to stupid jokes. It perfectly shows the hell that is high school (and society as a whole). Just like in high school, there are Marthas and Heathers everywhere in life.
J.D. is a great villain, because even though from his very introduction, we know he's a messed up person who does bad things, yet you start to empathize with him just like Veronica. It shows that, as a society, we go to great lengths to defend white men and their actions.
Heathers is furthermore also obviously a critique on the social hierarchies that exist in the world. It shows this on a smaller scale, high school. As J.D. nicely sums up towards the end of the movie: ".. because high school IS society". The Heathers rule the school and this movie really shows as to why that is. It's a system, that puts certain people at the top, like Heathers, and other _Martha's_ at the bottom. Murdering Heather Chandler might seem like a way to disrupt this hierarchy, and restore society to a pure form, but that is not the case. Heather Chandler does not equal her power, that's just a role she filled in the bigger system around them. Her being gone doesn't remove that role, it just passes it on to the next best fit.
In this movie, colors play a significant role. Heather Chandler being red represents anger and her dominance. Heather McNamara being yellow represents her kind soul, but also her weakness. Heather Duke's green represents her jealousy of Chandler. Veronica's signature color is blue which represents intelligence, but after having murdered Heather Chandler she wears a purple outfit. As you may know, blue and red make purple. I see this as Heather Chandlers 'evilness' affecting Veronica as well. Veronica might think she's rid the world of evil, yet she's simply become evil herself.
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