Hoot opens with a boy riding a horse through a majestic mountain background in Montana. We learn that the protagonist, Roy Eberhardt, has moved six times due to his father's job with the Department of Justice, and of all the places he's lived, he likes Montana best. So, of course, his father announces they're moving to Florida, to a town called Coconut Cove.
On his first day of school in Florida at Trace Middle School, Roy is harassed by the school bully, Dana Matherson, on the school bus. Dana shoves Roy's face up against the window, which allows Roy to catch his first glimpse of the "running boy", a blond-haired rather wild looking kid running as fast as he can with no shoes. Roy's interest is piqued, and he asks his new friend Garrett if he knows who the boy might be. No one seems to know.
Meanwhile, Curly (Tim Blake Nelson), a foreman at a local construction site for the new Mother Paula's Pancake House, has called the police over some vandalism. Officer Delinko (Luke Wilson) arrives and sees that someone is trying to slow down the planned bulldozing of the lot by removing survey stakes. Delinko catches his foot in a hole in the ground, and we see that it is the burrow of a burrowing owl.
The next day on the bus Dana resumes his bullying, and starts to choke Roy after Roy tries to brush him off, as he is watching for the running boy again. The boy runs by the bus again, and Roy decides to follow him, first punching Dana in the nose to escape him. Roy jumps off the bus and runs after the boy, bumping into a tall blond-haired girl on his way off. He chases the boy across several yards and a golf course, but loses track of him when a golf ball strikes him in the head. Roy wakes up at home and finds out that his parents have been notified by the school of the bullying incident, and that Roy has broken Dana's nose. His parents make Roy write a letter of apology in the hopes of clearing everything up.
Vandalism has struck again at the Mother Paula's construction site. This time all stakes were pulled up, and someone put alligators in the port-a-potties. Delinko decides to stake out the site.
At school, the girl who saw Roy chase the boy comes up to him at lunch and threatens him, warning that if "You know what's good for you, cowgirl, you didn't see anything." She is very strong, and Garrett informs Roy that her name is Beatrice the Bear, and she's a tough soccer player who even Dana finds intimidating. Realizing that Beatrice has some connection to the running boy, Roy decides to do some investigating of his own.
Delinko's stake out goes awry when he falls asleep in his police cruiser and someone spray paints all the car windows black; it is apparent that the vandal is the running boy. This gets into the newspaper and Delinko is demoted at the police station to driving a golf-cart vehicle. He becomes more determined than ever to catch the construction site vandal.
Roy and his mother go to Dana's house to deliver the letter of apology, and Dana vows to get even with Roy. Roy heads for the golf course where he last saw the running boy, and on his way passes the construction site and sees a den of burrowing owls. In the woods behind the golf course, he finds a campsite that appears to still be in use. He sees some clothing and a brown sack. He dumps the sack out and several cottonmouth snakes fall out. Behind Roy, the running boy appears and pulls him away from the snakes, then puts the sack over Roy's head so he won't see him, and ties his hands. He takes Roy back to the golf course and tells him to forget what he saw.
Roy takes an old pair of sneakers with him on his next search for the running boy. We see Beatrice bringing some food to the campsite and she tells the boy she can't cover for him forever. The campsite is next to an abandoned boat, where the boy is living. Roy approaches the hideout, and Beatrice heads him off, and asks him why he brought shoes. Roy says they're for the boy since he doesn't have any. Beatrice realizes that Roy is not going to give up, and tells him that the boy is her stepbrother and that he ran away from the military school his mother (her stepmother) sent him to because she doesn't like him. Beatrice's home situation in general is not good, and she is the only person her stepbrother will trust. Beatrice won't tell Roy her brother's real name, but says that she calls him Mullet Fingers.
Curly the foreman has been getting some very angry phone calls from Mr. Muckle, the Mother Paula's representative who is upset that construction is behind schedule. He orders Curly to get some attack dogs to patrol the site at night. It is revealed that Mr. Muckle knows about the burrowing owls, but he intends to ignore them and bulldoze the lot anyway. We are introduced to "Mother Paula", a B-movie actress who doesn't get along well with Muckle. A ceremony is planned for the groundbreaking of the new restaurant, and both Mother Paula and Muckle will be there.
Dana tries to beat up Roy the next day after school, but Beatrice stops him before things go too far and strips Dana to his underwear and ties him to a flagpole. Beatrice has been looking for Roy because she needs help. Mullet Fingers has been bitten badly by the attack dogs, though he succeeded in getting rid of them by putting the cottonmouth snakes into the lot. Mullet Fingers and Beatrice reveal that he's the one trying to stop the construction in order to save the burrowing owls, which are a protected species. They first tried sending a letter to Mother Paula's, but all they got was a form letter reply from Muckle. Beatrice and Roy take Mullet Fingers to the emergency room, where they give his name as Roy Eberhardt to avoid giving away that Mullet Fingers is a runaway. This leads to some confusion as Delinko tells Roy's parents he's been attacked by a dog and they rush to the hospital only to find that Roy is fine and Mullet Fingers has escaped from the hospital. Roy is forced to tell his father that he's protecting Mullet Fingers and that they're only trying to save the owls.
Roy checks in on Mullet Fingers the next day at his hideout, and he's feeling better. He takes Roy on a tour around the area in a boat, showing him all the wildlife that is being threatened by developers. Mullet Fingers says that the state is being bulldozed from one end to the other to build hotels and resorts for tourists, at the expense of the environment. Roy and Mullet Fingers go fishing, and Mullet Fingers catches a mullet fish with his bare hands, thus his name. At home that night, Roy asks his father how he catches bad guys at work, and his father says he usually catches them in their paperwork. After Roy's parents say goodnight, a voice speaks from under Roy's bead. It's Beatrice, who snuck into the Eberhardt house that afternoon and has been hiding under Roy's bed. Her father and stepmother had a huge fight and she had nowhere else to go. Roy says she's welcome to stay the night, and Beatrice finally starts to call him by his real name, instead of her usual "cowgirl" or "tex".
The next day as Roy bicycles past the construction site to see the owls, Dana catches him once again. Roy runs across the construction site with Dana in pursuit, but Dana trips and falls over an owl burrow. Roy gets away and Curly and Delinko arrest Dana, thinking they've caught the vandal. Delinko quickly begins to suspect that Dana might not be the culprit, as he is a delinquent but has no record of vandalism. He tests his theory by showing Dana an alligator. Dana freaks out, proving that he couldn't have been the vandal as the vandal handled alligators.
Mullet Fingers tries another method to stop construction, this time removing the bulldozer seat. Mr. Muckle and Mother Paula arrive in Florida, and Muckle announces that the groundbreaking ceremony has been moved up to today. The three kids overhear this and decide something has to be done right now. Mullet Fingers is all for more vandalism because he sees no other solution, but Roy says that the real problem is no one knows about the owls but them. They launch a plan to bring as many people as possible to the construction site. Beatrice calls the mayor, and Garrett calls the local media. Roy goes to the records office and asks to see the paperwork on the Mother Paula's construction. He finds that the environmental assessment record is missing, but the record clerk informs him that there's supposed to be another copy at the construction site. Roy announces to his marine science class (taught by Mr. Ryan, played by Jimmy Buffett) that he's got something he wants them to see at the Mother Paula's ceremony that afternoon after school.
Mr. Muckle tries to kill the owls at the site by spraying a fire extinguisher into the burrows. Mullet Fingers catches him in a fishing net and ties him up in Curly's trailer. Roy and Beatrice arrive with the crowd they've assembled right behind them. Roy finds the environmental assessment file in Curly's trailer and leaves it next to the tied-up Muckle. When Delinko and Curly find Muckle, Delinko reads the file and realizes that something is seriously wrong. The now freed Muckle hurries outside to the bulldozer.
The mayor of Coconut Cove is making a speech. Roy jumps onto the stage and tells everyone about the owls and that the Mother Paula's company is breaking the law. Muckle drives up in the bulldozer and declares that the owls are no longer here. Roy, Beatrice, and Mullet Fingers stand in front of the bulldozer. Roy pleads with everyone to be quiet, and then maybe the owls will come out. Delinko jumps onto the bulldozer and turns it off. The crowds is silent, and eventually several burrowing owls poke their heads out of their dens. Everyone exclaims in delight, and Delinko places Muckle under arrest. "Mother Paula", the actress, gets on stage and declares that the company is donating the land as an animal sanctuary, which is captured on camera.
The owls are saved, Beatrice and Roy become good friends, Delinko gets promoted, Muckle is sentenced to community service, Dana is sent to military school, Curly and "Mother Paula" get together, Roy's parents decide to stay permanently in Florida, and Mullet Fingers and Roy meet often to fish and hang out, and the movie ends with the two boys spotting a sign about the construction of a new resort along a stretch of beach. They start planning.
Our three heroes Roy Eberhardt aka Cowgirl (Logan Lerman), Beatrice Leep aka Bertie the bear (Brie Larson) and Mullet Fingers (Cody Linley) gather everyone for the ground breaking ceremony of the new Mother Paula's pancake house which is also where the burrowing owls are.
Officer Delinko (Luke Wilson) finds the missing environmental report paper that developer Mr. Muckle (Clark Gregg) tore from the building permit. It turns out the owls are on a protected species list.
Mother Paula (Jessica Cauffiel) donates the area to be an owl sanctuary and later hooks up with the groundskeeper Curly Branitt (Tim Blake Nelson) who has changed professions to a dog walker. Mr. Muckle serves time doing community service. Roy gets to stay in Florida looking out for other urban development with his friend Mullet Fingers.