The story takes place at East Great Falls High, ten years after the events of American Pie. The new protagonists of this movie are three brand new hapless virgins: Rob (Hall), Nathan (Horton), and Lube (Hardesty). One night Rob accidentally sets fire to the school library, and finds “the Bible” (or Book of Love), the creation of Mr. Levenstein (Eugene Levy). Unfortunately for them, the book is ruined. The book had incomplete advice and sends 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 Levenstein and all the other people who wrote in the book, and start the restoration.
The story begins with Rob entering his bedroom, and attempting to masturbate with a peanut butter and jelly sandwich (similar to the apple pie scenario in the first film). While he is doing this his dog, Frizzie, tries to eat the sandwich, and Rob’s little brother Cody takes a video of him receiving this unwanted sexual gratification. Later, Rob meets with his friends, Nathan and Marshall Lube, at school. Nathan reveals that his girlfriend, Dana, has pledged to abstain from sex until marriage despite the fact that she has already slept with six other people. Rob talks to Heidi, a girl he is attracted to, and Stifler. Stifler states that if Rob doesn’t make a move on Heidi, he will. In class, Lube has a vivid fantasy about a group of cheerleaders, particularly one named Ashley. Rob and Heidi meet later in the school library where she discloses that she is a virgin, and wishes to just “get it [sex] over with”. At the school dance, Nathan tries to get to second base with Dana, but only manages to offend her due to her abstinence pledge. Rob attempts to tell Heidi how he feels about her but is interrupted by Nathan and Lube. He eventually finds her in the library about to have sex with another student, and drops a lit candle in a bin in shock. This sets the library on fire, which sets off the water sprinklers.