Proluge, we veiw a familiar poacher angrily talking about how Thomas and Twilight's team foiled his plans of getting Marahute, and he wishes to seek vengeance on them.
In the tranquil town of Timberline, 900-pound (407 kg) grizzly bear Boog enjoys a captive, but happy existence and spends his day as the star attraction of the town's nature show with nights living the life of luxury in the garage of park ranger Beth, who raised him since he was a cub. Later, our heroes meet up with Boog. One day, the hunting fanatic Shaw drives into town with the one-antlered deer Elliot strapped to the hood of his truck. Boog frees Elliot at the last minute and against his better judgment, before Shaw can go after him. Boog never expects to see his "buddy" again. Elliot follows Boog home and finds him sleeping in the garage and starts to throw rabbits at the window. He tells him to be "free" from his garage captivity and introduces Boog to a world of sweet temptations outside of the garage that he has unknown. When Boog becomes intoxicated with sugar sweets, events quickly spiral out of control as the two ransack the town's grocery store. Elliot escapes before Boog is caught by a friend of Beth, police officer Gordy. At the nature show, Elliot who is being chased by Shaw, sees Boog who attacks him, causing the whole audience in the show to panic before Boog threatens to hurt Elliot. Shaw attempts to shoot Boog, but Beth sedates them with a tranquilizer gun before he could, thanks to Gordy. Shaw flees before he can arrest him for shooting a gun in the town. The two trouble-makers are released into the Timberline National Forest, only three days before open season starts, but they are set over the falls, where they will be safe. As our heroes follow closely behind.
Since he lacks any outdoor skills, Boog takes Elliot as his hapless guide to get him back home to Timberline to reunite with Beth. But in the woods, they quickly learn that it is every animal for itself. The two run into their share of the forest animals including skunks Maria and Rosie, ducks Serge and Deni, panic-stricken rabbits, the Scottish-accented squirrel, McSquizzy and his rogue gang, Reilly and his beaver construction worker team, a porcupine named Buddy who is in search of a friend and the herd of deer led by Ian and Giselle (who Elliot is in love with) With each adverse encounter, Boog learns a little about self-reliance and Elliot gains self-respect and they start to become friends. Mako then shares with the others that he thinks McLeach is back. However, McLeach learns of our heroes' presence in the forest and decides to join forces with Shaw in order to obtain them.
Day by day, Elliot attempts to lead Boog out of the forest, but it becomes evident that he has no clue where they are going. After winding up at Reilly's dam, James then decides to go up the dried up river to prove that it is the way to Timberline but then he sees McLeach's truck! He quickly races back but Boog and Elliot, accidentally make the whole dam collapse and a huge wave of water sweeps them away. James gets tuck on some dirt but Percy shunts him free and they and the rest of the team run away to try and get away from the huge wave. But as they race on they are confronted by Shaw and McLeach, Boog then loses Dinklmen as the current makes the doll flout out of Boog's paw. They ended up in a waterfall with the flood washes everyone in the forest before the water recedes. Boog then sees a teddy bear shape in the mud and thinks it is Dinklemen, but it turns out it is just a rabbit covered in mud.
At first everyone blames Boog who accuses Elliot of lying to him about leading him home. Elliot admits he thought that if Boog spent time with him, he would befriend him. Our heroes are devastated by Elliot's deed, so they decide to leave the 2 on their own. Boog leaves to unwittingly find Shaw's log cabin. Shaw returns along with McLeach and talks to his gun "Loraine" and says he would take back what is his, discovers him (like Goldilocks and the Three Bears), and pursues him to the city road where Boog happens upon the glowing lights of Timberline. Instead of deserting his companions, Boog helps the other animals defend themselves using supplies taken from Bob and Bobbie's (two "scientists" looking for Bigfoot) RV while their pet dachshund Mr. Weenie joins the wilds. The next day, Boog leads a rampage against the hunters, sending them running after McSquizzy blows up their trucks with a propane tank named "Mr. Happy". Shaw and McLeach return for a final battle and shoots Elliot in the process, which enrages Boog to tie up Shaw with his own gun. McLeach is close to killing some of our heroes, as a gunshot is heard, but it turns out to be from Willy and not McLeach as the said poacher falls to the ground, dead. Boog rushes over to Elliot's body but soon finds that Elliot survived the shot, only losing his second antler in the fight. Beth returns to take Boog back home where he will be safe, but instead he stays with his friends and all animals live in the forest.
During the credits, Shaw is seen tarred, feathered and tied on the top of Bobbie and Bob's RV, who believe him to be Bigfoot.
- Zecora, Stephen, Sharky, Mako, Willy, T.C., Hugs, Buzz, J.J., Socky, Skunky, 1206, The Miner Trains: (Steam Grindor, Steam Mech, Mucker, Steam Claw D., Steam Driller, Steam Sweeper, and Steam Exavator), Evan, Steamy, Puffy, Shai-Shay, Rattlesnake Jake, The Planet Trains: (Zip, Dazzlen, Dusten, Gustis, Rings, Uray, Tune, and Shiver), Dusty Crophopper, Bill and Ben, McLeach, and Joanna guest star in this film.
- McLeach and Joanna are working for Shaw in this film.