Veronica stops J.D. from blowing up the school, although he ends up committing suicide by blowing himself up. Veronica then seizes the mantle of "most popular" from Heather Duke and begins hanging out with the "losers" of the school.
In this dark comedy, Westerberg High is ruled by the popular "Heathers" - Heather Duke (Shannen Doherty), Heather McNamara (Lisanne Falk), and the leader Heather Chandler (Kim Walker), who always wears a red hairband as a symbol of her authority. The trio of girls also hang out with Veronica (Winona Rider), mainly because she can forge anyone's handwriting, which allows the Heathers to play cruel tricks on the "loser" students. Although Veronica sympathizes with the school losers, she also loves the acclaim that comes with being part of the Heathers. Its also worth noting that all the adults in this film are detached and incapable of connecting with the teenage youth.
A new kid, Jason "J.D." Dean (Christian Slater) gains notoriety when he takes out a gun and shoots blanks at two football jocks/bullies named Ram and Kurt after they threaten him. He is the son of a construction magnate who secretly blows up buildings or landmarks that prevent him from pursuing his development schemes. The dad usually places dynamite in the boiler room of the offending structure so the police will conclude the boiler accidentally blew up. J.D.'s mother committed suicide by walking into one of the buildings her dad had rigged to explode moments before the bomb went off. Veronica and J.D. soon begin having sex, with Veronica unable to control herself around him.
Heather Chandler takes Veronica to a party at a local college where Veronica is publicly embarrassed. The girls fight and Heather C. promises to ruin Veronica's reputation. Veronica confides in J.D. that she wishes Heather C. were dead and that everyone's lives would be better without her. J.D. convinces Veronica to stop by Heather C.'s house the next morning and give her a drink"hangover cure." J.D. actually fills the mug with drain cleaner, which immediately poisons and kills Heather C. once she drinks it (its a bit unclear if Veronica realized J.D. had poured the drain cleaner in the mug). Veronica uses her forgery skills to compose a suicide note in Heather C.'s handwriting. Veronica states that she believes the whole thing was an accident.
The scheme works well. Heather C. is more popular now more than ever, and people are incredibly impressed with the depth of her suicide letter. Further, people seem genuinely happier without Heather C. in their lives. Eventually J.D. "tricks" Veronica into helping him kill Ram and Kurt too, leaving a suicde letter blaming their deaths on having a taboo gay relationship. Veronica realizes she had really wanted them dead, but is disgusted by her dark impulses and breaks up with the ever-more unhinged J.D.
The deaths of Heather C., Ram, and Kurt make them into legends, with the suicide notes penned by Veronica giving the three teens the depth, intelligence, and soul that they lacked in reality. Almost all the adults try to capitalize on the suicides, with a band named Big Fun even writing a hit song based on teenage suicide. J.D., in an effort to win Veronica back, blackmails Heather Dean into filling the leadership void left by Heather C. Although initially hesitant, Heather D. soon dons the red hairband worn by Heather C. and begins making people miserable while also having the entire school sign a petition to have Big Fun play at their prom. One of the losers named Martha unsuccessfully attempts to commit suicide and is mocked for trying to copy the example of the deceased "cool kids." Heather D. even humiliates Heather M., and Veronica arrives just in time to foil Heather M.'s suicide attempt. Discovering that J.D. is behind all of this, Veronica fakes her own suicide and when J.D. finds her seemingly lifeless body, he confesses to her corpse that he intends to blow up the school.
Veronica arrives to school the next day and learns that the boiler room is below the gym where a pep rally is being held. Taking a gun, she goes down and confronts J.D., who has wired the school to explode. J.D. explains that he has posted the signatures of all the students from the Big Fun petition onto a suicide note. He believes that every school has Heathers, and always will. The only place everyone can be equal is in Heaven. Veronica shoots and wounds him and stops the detonation. J.D. then reveals he has strapped a suicide bomb onto himself. Veronica watches as J.D. explodes in front of her.
Veronica then goes back into the school and takes the red hairband from Heather D., stating that there is a new sheriff in town. She immediately approaches the "loser" Martha and starts talking with her, potentially beginning an effort to equalize the school hierarchy.