After their first year at different colleges, the guys reunite once again and plan their summer. Looking for a good idea, Kevin (Thomas Ian Nicholas) turns to his brother (Casey Afleck) for advices. His brother suggest spending summer in a beach house and throw a bunch of parties with the last one being the biggest. All 4 friends agree but soon realise that they're gonna need an extra man to invest too. Stifler (Sean William Scott), the oversexed college clown gets invited along by Kevin.After arriving in Grand Harbor they manage to find work painting a house (based on the Tuition Painters franchise) in the area together. Because the owners of the house are two hot women, Stifler assumes they're lesbians. When the women leave the house, Stifler goes in to try and find proofs. Unfortunately, the women return quickly and find the guys hidden in the house. Instead of calling the cops, they decide to make fun of the guys. Jim (Jason Biggs), Stifler and Finch (Eddie Kaye Thomas) end up performing "like for like" sexual acts on each other in return for being able to watch the girls doing the same thing. Meanwhile, Oz (Chris Klein) and Kevin take turns watching up a ladder and listening on the walkie-talkie also in the room. The conversation is accidentally picked up and heard by many other people in the neighborhood. The whole thing ends when the girls offer to have sex in front of them if the guys will go down on each other. Stifler accepts but Jim and Finch just run away.After this, many concurrent stories run at the same time, some interacting with each other, other staying mainly separate.Jim learns that Nadia (Shannon Elizabeth), his high school crush from the first American Pie film, is coming to visit him in August. Nervous and insecure about his sex skills, and wanting to impress Nadia and make sure she forgets about his poor performance in the first movie, Jim seeks out Michelle (Alyson Hannigan), the band geek, to ask for a review on his performance with her. He finds her at band camp and makes a fool out of himself in front of the audience when he pretends to be Petey, a mentally challenged boy who plays the trombone. Michelle reveals that Jim wasn't really good but also offers to teach him how to get better. At night, Jim tries to watch a porno but ends up mistaking a tube of lube with a tube of super glue, gluing his hand to his penis. After going to the hospital, Jim learns he shouldn't use his penis for a few weeks. Not long after, Nadia shows up a few weeks in advance and obviously looking to get naughty with Jim. Jim doesn't want to reveal what happened and search for an excuse to keep Nadia away for a while so he can heal. He turns to Michelle. They pretend to be in a relationship so that Nadia will not expect Jim to have sex with her. Meanwhile, Michelle teaches Jim a few tricks to be a good lover. When Jim realises he's ready for sex again, he and Michelle breaks up in front of Nadia in an over-the-top fashion. As soon as Michelle closes the door of the house, it is revealed that she had developped real feelings for Jim. Soon after, Jim realises that he has fallen for Michelle too. Even Nadia realizes this and tells him, "Go, get your band geek, and I will find mine". Jim goes and plays the trombone once more whilst Michelle is playing the flute at a major recital in order to show her that she is the one he wants to be with. He returns to the big party with Michelle as his official girlfriend.Oz is lonely, being away from his girlfriend Heather (Mena Suvari) who is studying in Spain. To work out their mutual sexual frustrations from being away from each other, they proceed to start having phone sex. Unfortunately, they are interrupted by Heather's roomates the first time. And by Stifler very undiscreetly listening to the conversation the second time. They both resign themselves to wait for Heather's return. Unable to wait any longer, Heather grabs an earlier flight and surpises Oz at the party.Finch has become involved in the sexual art of Tantra, and claims that through Tantra he can "make an orgasm last for days". He is waiting for Stifler's Mom (Jennifer Coolidge), whom he had sex with in the first film, hoping she will show up and be willing to do it again. When Stifler is talking on the phone and seems to invite someone to their house, Finch assumes it's Stifler's mom, but it turns out to be his little brother Matt (Eli Marienthal), the star of later films. Finch is frustrated, but accept his fate. He spends the big party surrounded by girls and chatting with them. Even though he doesn't get any action, he seems happy.Matt, Stifler's brother, is having a lousy night at his brother's party when Stifler gives him a walkie-talkie and throws him outside to look out for cops. Being bored, he starts playing with the talkie, not knowing that one of the talkies is still at the ''lesbians" house. The girls starts answering Matt. The conversation is not revealed, but Matt shows up at the party with both girls at his arms. Stifler makes fun of him for getting lesbians untill one them says: "Who said we're lesbians?". Stifler understands they're not lesbians and begs to have sex with them. The girls agree. Stifler allows his brother back in the party and leaves with both women.Meanwhile, Kevin spends most of his time trying to understand the new terms of his relationship with his ex-girlfriend, Vicky (Tara Reid), as just friends. He doesn't end up "getting off" with anyone, but he does seem to succeed in getting over her.The geeky Sherman (Chris Owen) gives up on getting anyone after he is turned down by the experienced and savvy Jessica (Natasha Lyonne). In his depressed state, he starts a conversation with Nadia who has just let Jim go. While talking, she finds herself turned on by his "Sherminator" gimmick, and they run together to have sex somewhere.The morning after the big party, the guys are packing the car to return home when a car stops by. Driving the car is Stifler's mom. Finch exchange a few words with her and jumps in the car. They drive off together, unbeknownst to Stifler who just sees the car driving away. When Stifler realises that Finch is missing he finally understands what just happened.