The Chipmunks - Alvin (Justin Long), Simon (Matthew Gray Gubler), and Theodore (Jesse McCartney) - are making a video for Dave's (Jason Lee) birthday. The Chipettes - Brittany (Christina Applegate), Jeanette (Anna Faris), and Eleanor (Kaley Cuoco) - thought it was a going-away party for them since they're gonna go to judge "American Idol", but they join in the fun. The rodents throw a huge party, with Redfoo being the DJ. Dave comes home and sees the party before pulling the plug.
Dave has made the boys settle into a normal life and leave their performing days behind them, to their disappointment. He is set to head to Miami to help produce a record for pop sensation Ashley Grey (Bella Thorne). Despite being upset with the Chipmunks, Dave takes them mini-golfing. Simon is trying to get a good swing, but he's taking too long. Alvin pushes him, and Simon nearly gets the ball in until a teenager named Miles (Josh Green) ruins the shot for him. Dave returns with his girlfriend Samantha (Kimberly Williams-Paisley). The boys like her until they discover that Miles is her son. Dave and Sam leave the boys with Miles, who takes pleasure in tormenting them throughout the afternoon.
The Chipmunks join Dave at the recording studio with Miles as they are checking out Ashley record her new album. Miles has a crush on her so he's awkward around her when he's not bothering the boys.
At home, the Chipmunks see that Dave has brought home a bag with an engagement ring in it, making them think that Dave is going to propose to Sam. They try and sneak into his room at night and steal the ring, but they fail. The next morning, Dave heads out to Miami with Sam and leaves the boys with Miles to be checked up on by their neighbor Ms. Price (Jennifer Coolidge). The boys all conspire to stop the proposal so that they don't have to deal with each other, and for fear that Dave will abandon the Chipmunks should he and Sam have kids of their own. Alvin finds three squirrels and drugs them with cough syrup, then dresses them up in his and his brothers' clothes to fool Ms. Price.
The boys go to the airport. Alvin and Simon sneak in through the luggage while Theodore is in cargo. The TSA officer (Uzo Aduba) stops Miles and searches him. Simon is in his pocket and gets nervous, peeing down Miles' leg and dropping a turd, which lets them go. On the plane, Theodore lets a monkey out of its cage, but that monkey lets the other animals loose. The Chipmunks are caught by Air Marshal James Suggs (Tony Hale). The plane makes an emergency landing in Texas. The boys are detained in Suggs' office, and he reveals he has an axe to grind with the Chipmunks since his girlfriend broke up with him and told him to grow up for having so much Chipmunk merchandise (it also didn't help that their Christmas song was playing when she dumped him). The boys leave the office and are subsequently pursued by Suggs.
The boys are dropped off by a taxi at a bar. They're not allowed in since they're all under 21, but they're allowed to stick around when they say they can perform for the bar. With Miles on the guitar, they all play a song that pleases the crowd. However, the fun is ruined when Suggs arrives. The Chipmunks hide in a man's beard, which Suggs grabs onto and causes him to incite a bar brawl. The boys escape in a taxi as Suggs runs after them.
Since they can't pay the cab driver, the boys get kicked out and are left in the middle of the road. They rest under a tree for the night and bond with Miles as he mentions how he grew up without a father.
The next day, the boys all continue moving and get money to ride a bus to New Orleans in time for Mardi Gras. Unfortunately, Suggs has caught up with them. The Chipmunks then start a performance to "Uptown Funk" (sorry, "Uptown Munk"), getting the whole crowd crazy. Meanwhile, we see Dave and Sam having fun in Miami until they see footage on the news of their boys in New Orleans.
Dave and Sam find the boys at the airport and scold them for disobeying them and getting into trouble. The Chipmunks discover that they're on the no-fly list, so Dave has to drive them back to Miami. Suggs gets his own car and drives down there himself.
Dave leaves the boys in a hotel room to await the babysitter while he goes to a restaurant to meet with Sam. He takes the ring box with him, but Alvin took the ring out when he wasn't looking. He and his brothers celebrate, but Miles is hurt since he felt that he grew close to the Chipmunks and is upset that they're celebrating the sabotage of the proposal. He leaves the hotel with his earphones in and crosses the street, unaware that a car is headed toward him. Alvin and Simon hurl Theodore toward Miles to push him out of the way, and the car hits Theodore instead. He is hurt but turns out okay when he smells food. Miles thanks him for saving his life, and they head to the restaurant to give back the ring.
Suggs find the Chipmunks and chases them into an elevator. When it looks like he's got them, they turn the tables on him and leave him trapped in the elevator by turning off the power. They head to the restaurant and get to Dave's table where Alvin spills the beans on the proposal. However, Dave says the ring wasn't his, but for his work friend Barry (Eddie Steeples) to give to his girlfriend. That proposal is ruined when Barry gives his girlfriend a box with a breath mint in it. Dave and Sam agree that it's too soon for them to get married and that they're enjoying their time together, but Dave is disappointed in the Chipmunks.
The Chipmunks find the Chipettes and head with them to a club where Dave, Sam, and everyone else is. The rodents help Barry re-propose to his girlfriend, and she says yes. They then perform a song with Miles and Ashley, which is a hit that puts the Chipmunks back in the spotlight. After the performance, the Chipettes say goodbye, and Miles and Ashley make plans to hang out at an afterparty.
On the road trip home, Dave stops at a courthouse and legally adopts the Chipmunks after they discuss their misunderstanding. They make it home, and Dave says that nothing can ruin the day for him. That is, until they get inside and the boys remember the squirrels, all of whom destroyed everything in the house. Cue "AAAAAALVIIIIIIIIN!"
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