Napoleon Dynamite (Jon Heder) is an eccentric high school student from Preston, Idaho who lives with his grandmother (Sandy Martin), his older brother Kip (Aaron Ruell) and their pet llama, Tina. Kip, 32, is not currently employed and boasts of spending hours in internet chat rooms with "babes" and training to be a cage fighter. Napoleon daydreams his way through school, doodling ligers and other fantastic creatures and being bullied.
Napoleon's grandmother breaks her coccyx in a quad bike accident and, believing her grandsons cannot be trusted to look after themselves, asks Uncle Rico (Jon Gries) to stay with them while she recovers. Uncle Rico is in his 40's and a former high-school quarterback who lives in an orange 1975 Dodge Santana campervan. His presence, although increasingly irksome to Napoleon, is a boon to Kip as he and Uncle Rico embark on a joint project to become door-to-door salesmen. Kip reveals that he would like to earn some money to enable him to meet his new internet girlfriend from Detroit, LaFawnduh Lucas (Shondrella Avery). Uncle Rico is not averse to using Napoleon's name to gain credibility in his attempts to sell herbal breast-enhancement products to Napoleon's school mates, causing increasing friction between Uncle Rico, Napoleon and Deb.
Napoleon makes two new friends at school, Deb and Pedro. Deb (Tina Majorino) is a shy and sensitive girl. The two have a falling out when Uncle Rico attempts to sell her breast-enhancement herbs and implies that Napoleon suggested it. Pedro (Efren Ramirez) is a transfer student from Juárez, Mexico, who decides to run for class president against popular girl Summer Wheatley (Haylie Duff). Despite a couple of hiccups, the campaign goes well until the time Pedro is about to deliver his final speech, when he discovers that each candidate must perform a skit afterward. Having not prepared a routine, a despondent Pedro gives a lackluster speech, believing that his candidacy is over. Napoleon gives a music tape he had received from the visiting LaFawnduh to the sound engineer and performs a dance routine (to "Canned Heat" by Jamiroquai), which wins a standing ovation from the school audience.
The film closes out with a montage of scenes showing a happy ending for all concerned. Pedro wins the class presidency. LaFawnduh, smitten with Kip right from the start, transforms his fashion, and they leave town together. A fully recovered Grandma returns and has clearly missed Tina, the llama, more than her grandchildren. Uncle Rico's girlfriend returns to Rico, and while Napoleon is playing tether ball by himself, Deb shows up and starts playing with him, having forgiven her friend.
A post-credits scene, added after the festival release, reveals Kip and LaFawnduh getting married. Napoleon is noticed as missing by Pedro and Uncle Rico, but as Kip sings for LaFawnduh, Napoleon rides up to them on a brown horse, and says that he has tamed a wild honeymoon stallion for them, which they use to leave their wedding.
