Some time after the events of the previous film, a very disfigured Paul (Rider Strong) escapes from the creek and wanders through the woods, leaving pieces of his own flesh along the way. When he finally manages to make it to the highway, he is splattered and killed by a school bus. His remains are checked by Deputy Winston Olsen (Giuseppe Andrews), the local policeman from the previous film. Winston assures the shocked bus driver that he has hit a moose.
The creek Paul was lying in turns out to be connected to a bottled-water company and the infected water was distributed to the local high school.
John (Noah Segan), a senior at the high school, is deciding whether to go to prom with his long-time crush Cassie (Alexi Wasser) or stay home. His friend Alex (Rusty Kelley) is against going until he hooks up with a girl named Liz (Regan Deal). She says if she can get off work that night, she will meet him there.
John asks Cassie to go to prom but she refuses. Meanwhile, Winston is at a restaurant where a worker from the bottled-water company dies from the infection. He then realizes the creek got heavily contaminated and goes to the water plant to tell the officials that the water is contaminated. The worker he informs is quickly killed by a group of CCD (Contamination Control Division) soldiers in NBC suits. Winston leaves before they can get to him.
At the high school the infection begins to spread slowly. Frederica (Amanda Jelks) dies in the swimming pool from the infection and Rick (Thomas Blake, Jr.) is killed when he drowns after hitting his head on the side of the pool and falling in. Alex is disappointed that Liz did not come, while John gets into a fight with Cassie's boyfriend Marc (Marc Senter). Principal Sinclair (Michael Bowen) then kicks John out. Cassie follows him and John angrily confesses his love to her. As popular girl Sandy (Lindsey Axelsson) is declared prom queen the CCD then forces John and Cassie back into the school. The CCD locks all of the main exits from the school and kill Principal Sinclair when he demands to know what is going on. The infection then begins to kill the students in the gym at an alarming rate. The gym is then gassed from the outside. Cassie, John, and Alex watch in horror as all the students are killed. Winston is picked up by his cousin Herman (Mark Borchardt), ready to leave town.
Alex discovers he is infected and that the disease is incurable necrotizing fasciitis. The only way to stop the infection is to amputate the infected limb. However, Alex's infection is already too severe and he stays behind. John begins to show signs of the infection too and lets Cassie amputate his hand to stop it.
Cassie's boyfriend Marc then comes out of nowhere, hits Cassie with a hammer, and tries to kill John but Cassie recovers and kills him with a nail gun. The two leave the school only to be ambushed by the CCD. John stalls them, allowing Cassie to escape. She finds herself on the highway and stops Herman's van. Winston and Herman take Cassie with them. The camera shows her back where she is starting to show signs of infection.
Meanwhile, Alex's date Liz is at her workplace. She is a stripper at Teazers and she spreads the infection to the customers, who in turn spread it further around the country and even to Mexico.
In a post-credits scene, Darryl and Dane are shown watching a movie and Dane says "prom blows".
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