Yogi (Voiced by Dan Aykroyd) and Boo Boo (Voiced by Justin Timberlake) are two brown bears who have a penchant for stealing picnic baskets from visitors to Jellystone Park, while park rangers Smith (Tom Cavanagh) and Jones (T.J. Miller) are preventing them to do so. Meanwhile, Mayor R. Brown (Andrew Daly) realizes that Franklin City is facing bankruptcy due to profligate spending on his part. To solve it and fund his election campaign to be the next governor, the mayor decides to select Jellystone as a logging site, and Jellystone is prepared to be shut down.
To save the park, Ranger Smith and his love interest, a woman named Rachel (Anna Faris), who was currently in Jellystone to film a documentary, hold a Centennial festival where Smith hopes to make a profit selling Season Passes. To sabotage the effort, Mayor Brown plays on Ranger Jones’ desire to be head ranger and promises him the position if the funds are not raised. Yogi and Boo Boo had promised Smith to stay out of sight during the festival, but Jones convinces them otherwise. They try to please the crowd with a waterskiing performance, but Yogi inadvertently sets his cape on fire, causing the fireworks Smith set up to be knocked over and ignited prematurely, launching them into the crowd, who flee in a panic. After Jellystone is shut down, Ranger Smith is forced to stay in Evergreen Park, a small urban enclave choked with litter and pollution, but not after he tells Yogi that Yogi is not as smart as he thinks he is.
Now seeing that their home is in danger of being destroyed, Yogi and Boo Boo travel to Evergreen Park and tell Smith about this, where he places the clues that Mayor Brown had given him, that Brown and his chief of staff (Nate Corddry) are planning to cut down Jellystone and its trees to make money. They return to Jellystone, and along with Rachel plan to stop the sale of the park. They learn that Boo Boo’s pet turtle is a rare and endangered species, which means that, by law, the Park cannot be destroyed if the turtle is residing there. Ranger Jones then turns against Mayor Brown and teams up with Smith, Rachel, and the bears, after learning that he has been manipulated. Mayor Brown learns about this and has his guards steal the turtle so he can continue with his plan of shutting down Jellystone, confessing to the group that power is more convincing than the law.
After Mayor Brown leaves for his conference, Rachel reveals that she had installed a camera in Boo Boo’s bow tie, which recorded Mayor Brown’s confession. The turtle manages to escape from Brown’s Chief of Staff by using his frog-like tongue to pull itself through the car window and out into the park. Yogi and Boo Boo keep the guards distracted so Ranger Smith can upload the confession in the Jumbotron. When the confession is played, the crowd riots, and Brown attempts to tell them that the turtle does not exist, but the turtle manages to get into the conference. The people then learn about the park having an endangered species. Police officers arrest Mayor Brown and his guards for his crime; his chief of staff attempts to escape, but is pinned down by Rachel and he’s arrested as well.
Jellystone Park is reopened and becomes a great success. Jones loses his position as head ranger and Smith takes it back, but Jones still works there, handing out flyers about how Jellystone Park has a rare and endangered turtle. Rachel and Ranger Smith admit their feelings for each other, but after they kiss, however, they start chasing after Yogi and Boo Boo, who are back to stealing picnic baskets once again.