Roy Eberhardt has just moved to Florida in the town Coconut Cove. He then starts being bullied by Dana Matherson. One day on the school bus, Roy sees a boy running near the bus barefoot. He tries to get off the bus, but Dana grabs him by the throat and starts choaking him. Roy escapes by punching Dana in the face, accidentally breaking his nose, but cannot catch the running boy because he is hit in the head by a golf ball while trying to follow him. Roy is suspended from the bus for two weeks and is told to write an apology letter to Dana. Roy tries to call a truce with Dana, but Dana refuses.
Mother Paula's All-American Pancake House Corporation intends to build a pancake house in Coconut Cove. The bulldozers have already been parked on the construction site, but work is delayed over and over again because of bizarre but effective acts of vandalism that occur in the night. Roy learns this is the work of the running boy he only knows as "Mullet Fingers", whom he befriends (his step-sister happens to be Beatrice Leep who also befriends Roy). His motives for the vandalism are honorable; Mullet Fingers wants to save the endangered burrowing owls that live on the site from being killed when the bulldozing begins.
The construction foreman on the site denies the existence of the owls. Roy attempts to help Mullet Fingers prove the owls are on the site, including loaning him a digital camera. In his current events presentation, Roy tells his history class about the owls and how the pancake company will bury them, and encourages them to join him in protesting at the ground breaking the next day.
Roy and Beatrice and other students attend the ground breaking, where they expose the company's greed and dishonesty to the entire town. The young people succeed in exposing the illegal acts of those in power, including illegally removing an environmental impact statement from the official file. They save the birds and their habitat. The president of Mother Paula's All-American Pancake House blames former employees and promises to preserve the property as an owl sanctuary.
Mullet Fingers' mother sees him there protesting with Roy and Beatrice and takes him home telling reporters she loves him, which is a complete lie. In an effort to escape his family only two days later, he climbs out of a bathroom window with Beatrice's help and is accidentally mistaken for a burglar. When Mullet Fingers' mother spitefully tells the police that he stole a ring from her, he is sent to the same juvenile detention center as Dana. Mullet Fingers escapes the jail using Dana as a distraction. At the end, Roy discovers that Mullet Fingers' real name is Napoleon Bridger.