The film takes place one year after the events of the first film.Elliot (Joel McHale) has grown giant new antlers and is getting married to Giselle (Jane Krakowski). But during a mishap, Elliot’s new antlers are cracked off and now look like they did in the first film, which upsets him. Luckily, Boog (Mike Epps) and the others manage to cheer Elliot up by having a rabbit fight. But Elliot has new emotions about his marriage and feels reluctant to marry Giselle. Mr. Weenie (Cody Cameron) finds a dog biscuit trail that his previous owners left behind and uncontrollably follows it. At the climax of the wedding, Elliot witnesses Mr. Weenie being taken away by his old owners, Bob and Bobbie (Georgia Engel). Elliot tells the story to the other forest animals (a little overreacting) and decides to make a rescue mission to save him. The other ones that go on Elliot’s rescue mission are Boog, Giselle, McSquizzy (Billy Connolly), Buddy, (Matthew W. Taylor), and Serge (Danny Mann) and Deni (Matthew W. Taylor).
Meanwhile, the other pets meet. There is Fifi (Crispin Glover), a toy poodle and his basset hound companion Roberto (Steve Schirripa), two cats named Stanley (Fred Stoller), whose companion is a mentally retarded cat named Roger (Sean Mullen), and a Southern dog named Rufus (Diedrich Bader), whose companion is his girlfriend Charlene (Olivia Hack). Fifi discusses his hatred for wild animals as one night he goes into the bushes to retrieve his chew toy and is shocked by the wild animals inside, and accidentally gets his tail touched by the bug lighter. He then tries to maul a nearby rabbit, until stopped by his owner. Meanwhile, the wilds find Weenie, much to Elliot’s dismay, who does not want to marry Giselle. They try to free him while his owners are in a gas station. They free him from his chains, but accidentally leave him stuck on the RV along with Buddy. Elliot and Giselle get in a feud, and eventually leaves Elliot to search for Mr. Weenie himself, while Serge and Deni fly to look for him.
The owners reach the pet camp with Mr. Weenie and Buddy, unbeknownst to them. The other pets meet with Weenie, and Fifi tries to change Weenie back into a pet, but fails. Buddy helps Weenie escape and Buddy tries to free Weenie from his shock collar. During the chase, Fifi gets shocked by the collar and gets his forehead burned, which causes him to lose most of his sanity. Meanwhile, Serge and Deni return and explain they found Weenie and Buddy at a pet camp, which they now escaped from. Boog and the others set camp at a human camp, and Boog tries to convince Giselle that Elliot is a good person and they are good together, but fails. Elliot, meanwhile, is having a horrible time, following his own tracks that he confuses for Mr. Weenie’s and gets his head stuck on a trash can lid with gum on it, but misses his friends and becomes a mess. The wilds reach the pet camp, but the pets and their owners have already left, but realizes that they have gone to Pet Paradiso, a vacation spot for pets. Elliot finds Weenie and Buddy and is convinced to go to Pet Paradiso to save his friends.
The wilds reach Pet Paradiso and try to sneak in by disguising themselves as pets, with Giselle as a dalmatian and McSquizzy as a chihuahua. Boog attempts to sneak in as a cat, but gets the idea to be a sheepdog. Elliot also disguises himself as Boog’s female human owner. Giselle and McSquizzy walk around Pet Paradiso looking for Mr. Weenie, but their cover is blown and are kidnapped by Fifi and the other pets. Elliot, Boog, Buddy and Mr. Weenie attempt to go inside to save Giselle and McSquizzy, but are captured by Fifi as well. Fifi tries to kill them with a pile of shock collars. As Boog tries to stop Mr. Weenie from going down a waterslide, his cover is blown as well and the security try to tranquilize him after he causes a rampage after people confuse his weight. Before Fifi shocks the wilds into submission, Elliot tries to profess his love for Giselle, but fails. As Fifi is about to fry the wilds, Boog was chasing Weenie down a waterslide, enters the pets’ lair, and the water that was rushed from the waterslide forces everyone out of the lair.
A battle between the wilds and the pets ensues, with the Pet Paradiso security focused on tranquilizing the wilds. Elliot saves Giselle and accidentally places all the shock collars on himself. He also wrestles Fifi in the pool for the shock collar remote. Fifi eventually grabs the remote and activates all the shock collars, but does not realize that Elliot put all the shock collars on him. Fifi survives, but the explosion caused him to lose his hair and become bald, resulting in him being humiliated and laughed at by other pets. The pets and the wilds settle their differences and decide to become friends. Mr. Weenie decides to join the pets and returns to his owners in rejoice. Elliot finally professes his true feelings for Giselle, and they get married.