When they lose the nut shop in a freak accident, the park animals return to Liberty Park in time to learn that the greedy Mayor wants to turn it into an amusement park and must team up with a gang of kung fu street mice in order to save their home.
In the start of the film, Surly tells the audience how hard it is to be a little guy with a lot to worry about in the world, like bikes, cars, bubble gum, but then things changed last summer when the nut shop is closed down and a lifetime supply of food is left in the basement. Surly, now loved and adored by all the park animals due to Grayson stepping down to let him be the park hero/leader (possibly out of sheer guilt) and he starts out by doing a cannon ball into a nut barrel. As he checks on everyone, it is discovered that all of the park residents have grown to living off free food for so long that they barely remember how to get it the old fashioned way.
Andie tries to help them remember by teaching a group of chipmunks how to forge for a nut, but after her own nut gathering plan backfires and causes her to fall from the tree, the chipmunks to back to the store, much to Andie's annoyance. During a nut eating contest, Surly tries to win over Andie with her favorite nuts, Brazil nuts but she refuses and tells them to go back to the park since life in the shop is turning them lazy, spoiled and fat.
Andie unexpectedly gets her wish when Mole, who's job it was to make sure the boiler in the basement is shut off before leaving, accidently leaves it on, which causes it to explode and destroys the nuts and the shop at the same time. Unwilling to admit defeat, Surly goes with Buddy to find more food but every attempt backfires and they go back empty handed.
Andie tries to inspire them to go back to their roots but is interrupted when the town's mayor suddenly rolls in and in front of a group of reporters, he tells them that he is going to replace Liberty Park with Liberty Land, an amusement park of his own design that promises to be more fun then a regular old park.
Surly decides to fight back instead of leaving and everyone rallies with him. Eventually with enough team work, they chase the workers away. That night Andie gives them stale nuts to eat which they enjoy (although it more of desperate hunger then anything else) and Surly and Andie talk about losing the shop and how to get by without it even thought the purple squirrel is convinced that they won't. The next morning Andie tells the animals that Surly has lost his animal survivor skills, which insults Surly and he goes to find nuts but gets caught in a trap set by Gunther, head of an animal control team the mayor hired to get rid of the animals.
The situation gets worse when Precious defends her friends by luring Frankie away from them, and is disgusted that the French Bulldog is in love with her but the plan backfires when Heather, the mayor spoiled daughter, takes Precious with her and Frankie and the animal control force the animals out of the park, which is then destroyed and the construction begins with broken rides that are condemned in place of real rides due to them being cheaper then more functional rides. Surly and Buddy go after Precious to rescue her while Andie, Jamie, Jimmy and Johnny go to find a new home but both their plans for a new home are dashed when the only 'park' turns out to be a dangerous golf course that almost kills them.
Meanwhile Surly and Buddy run into Mr. Feng and after Surly accidently insults him, they run for their lives but manage to escape his wrath before they make it to the mayor's mansion where they find him talking about buying such dangerous rides only to gain more money from people, throwing away safety and everything else out the door. Precious and Frankie are tormented by Heather who treats them like toys instead of pets and when Surly and Buddy rescue her, she tells Frankie the truth before she realizes that she does care for him. However before there's time for second thoughts, Surly accidently steps on a loud toy which alerts Heather and they run for their lives. While avoiding Heather and the Mayor, Surly purposely stops to destroy the mayor's favorite bobble head and the mayor shoots them with a bow and arrow. Although it misses Surly, the arrow hits the platform Buddy is standing on, causing the rat to fall to the streets and into a coma, much to Surly's horror.
Andie watches the making of Liberty Land before Surly comes carrying a limp Buddy in his arms. As Andie and Surly carry the comatose but respiring Buddy inside the remains of the nut shop and lay him on a big slab, Surly blames himself for his recklessness and tearfully laments about the times he and Buddy had together, especially their first meeting when both he and Buddy were young and saved each other from a hurricane, which led to their brotherly bond. Andie then tries to convince Surly to come up with a plan to end LIberty Land, but Surly still feels responsible for Buddy's near-death state, saying his crazy schemes do not work. Precious licks Buddy out of thanks, and it suddenly causes the unconscious rat to move. Surly sees this and tells Precious to lick him more times. Sure enough, Buddy miraculously wakes up and Surly hugs his best friend tight, apologizing for being reckless and is inspired by the others to try again but this time they won't stop until the park is back.
At the opening of Liberty Land, the mayor's greed and carelessness is shown to the reporters, especially one who dismisses the whole thing as an environmental disaster. Ad the mayor and his supporters party, the animals suddenly attack and drive the humans out, but animal control comes to capture them. One by one, they manage to succeed and Surly realizes they need more help. With him the last one standing, Surly goes to Mr. Feng who tries to kill him but Surly's plea for help and reasoning that no matter what all animals are just animals who need help from each other as well as him saying that without his friends he has nothing to live for he spares Surly and agrees to help him.
Surly and Mr. Feng help Andie and the others escape the exterminations truck and go back to trash the amusement park, which attracts the attention of the police, who arrest Gunther and Heather for animal abuse when they try to dart Precious and Frankie only to end up darting Heather by accident. To avoid being sent to jail, the mayor tries to escape using a hot air balloon but Surly and Buddy use a roller coaster to catch up. Buddy slings Surly to the balloon where they battle and Surly manages to win by using the mayor's own umbrella/cane against him, sending him flying and landing on a bouncy house where Mr. Feng and his army bite him and the police arrest him.
Andie uses a forklift to destroy the roller coaster as a sign of victory and kisses Surly, who adores the kiss before he ends up being kissed by Buddy, Precious and Frankie. With the mayor gone, the humans of the city rebuild the park in a mater of weeks. During that time the animals finally go back to gathering food for themselves, Mr. Feng and his army move into the park to practice Tai Chi and Frankie and Precious have three bouncy little puppies who deem Surly their uncle.
Surly finds a nut cart and wants to raid it just like old times and, much to his surprise, Andie wants in as well. He whistles to Precious and both squirrels ride on their pug friend to raid the nut cart for it's loot.
- Will Arnett as Surly, a purple squirrel who was at first loathed by the park's animals, but is now considered a hero for helping to save them from a dire food shortage that he had unintentionally caused.
- Justin Felbinger voices a younger Surly.
- Maya Rudolph as Precious, a pug who was formerly owned by bank robbers but is now currently the park animals' loyal friend and protector and Frankie’s wife.
- Jackie Chan as Mr. Feng, the Chinese-accented territorial leader of a gang of white street mice, who hates being called cute due to his small size and big eyes.
- Katherine Heigl as Andie, a compassionate red squirrel.
- Bobby Moynihan as Mayor Percival J. Muldoon, the unscrupulous mayor of Oakton City and the father of Heather who plans to replace Liberty Park with a faulty amusement park named Libertyland.
- Bobby Cannavale as Frankie, Heather's former pet French bulldog, who falls in love with Precious. In the end, he becomes her husband.
- Isabela Moner as Heather, Mayor Muldoon's spoiled and vociferous daughter.
- Jeff Dunham as Mole, a mole who formerly worked for Raccoon and now works with Andie.
- Gabriel Iglesias as Jimmy, a groundhog who is Johnny and Jamie's brother and the leader of the Bruisers (consisting of him and his siblings).
- Sebastian Maniscalco as Johnny, a groundhog who is Jimmy and Jamie's brother. He was previously voiced by Joe Pingue in the first film.
- Peter Stormare as Gunther, a Swedish-accented deranged animal control officer.
- Kari Wahlgren as Jamie, a groundhog, who is Jimmy and Johnny's sister. She was previously voiced by Annick Obonsawin in the first film.
- Dwayne Hill as Police Officer, a police officer who inspects Liberty Park on opening day. He was previously voiced by Scott McCord in the first film.
- Laraine Newman as Daredevil Chipmunk, a chipmunk with a daredevil personality that lives in Liberty Park.
- Cal Brunker as Charming Chipmunk, a chipmunk with a charming personality that lives in Liberty Park.
- Julie Lemieux as Li'l Chip, a chipmunk that lives in Liberty Park.
- Bob Barlen as Handsome Mouse
- Jess Harnell, Fred Tatasciore, and Andrew Ortenberg as Animal Control Officers, fellow workers of Gunther who help to round up Surly and the Park Animals.
- Greg Chun and Dave Fennoy as Mouse Henchmen, white street mice who have brown eyes like the rest of his group.
- Robert Tinkler as Redline, a blue mouse whose catchphrase is "We're all gonna die!"
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