The story takes place at East Great Falls High, ten years after the first American Pie movie. The new protagonists of this movie are three brand new hapless virgins: Rob (Bug Hall), Nathan (Kevin M. Horton) and Lube (Brandon Hardesty). One night Rob accidentally sets fire to the school library, and finds the bible, Mr. Levenstein's (Eugene Levy) creation. Unfortunately for them, the book is ruined. The book had incomplete advice, and embarks them on a helpless journey to lose their virginity. After trying and failing for most of the time, they pledge to restore the book, and to do this, they must find the original author of the book (Levenstein) and all the other people who wrote on the book, and start the restoration.
The film was said to be the most similar to the original trilogy, with three new 'hapless virgins' and a copy of the original Stiffler.