At an arena for a charity benefit rock concert, the Chipmunks are performing and the crowd goes wild. Alvin takes the lead, and then begins to show off, and Dave (Jason Lee) calls him over and tells him to stop it. He reminds him that this is a charity event, and not all about Alvin, and to stop it, but Alvin refuses. He slings the cord to his electric guitar over a high beam, and swings over the crowd while playing his guitar. Inadvertently, Alvins cord knocks a huge Alvin-cutout loose, and it hits Dave. Dave is taken to the hospital, and is covered in gauze, a neck brace, and traction and casts on every limb.
Before going under sedation, Dave tells the chipmunks that Aunt Jackie (the one Theodore calls Popcorn Jackie since she sends them popcorn) will take care of them, and that he has arranged for them to go to school. Lastly, he puts Simon in charge and tells them to be good.
The chipmunks fly home, and see Popcorn Jackie waiting for them with cousin Toby (Zachary Levi). Toby neglects to set the brake on her wheelchair, and she rolls backwards down 2 flights of stairs, and out the doors. An ambulance takes her, and Toby says hell watch the boys.
At home, he tells the boys to stay out of trouble, while he is busy playing video games. They play around and eat junk food since no one is watching. Dave calls, and Alvin decides not to tell him about Jackies accident, and hangs up on him quickly. As usual, Theodore wakes up at night from a nightmare, and goes into Tobys room and asks if he can stay there. Toby agrees, and tells him that chipmunks dont have anything to fear but eagles. Eagles with large talons that want to catch and eat chipmunksthis scares Theodore, and he runs out of Tobys room. Now Theodore is scared of eagles.
Toby takes the boys to school, and drops them at the curb. They walk in, and are nearly stepped on amid the chaos of the high school hallways. Theodore sees the school mascot is an eagleand remembers Tobys story, and runs away, scared. In homeroom, all the girls in the class go mad for the chipmunksand leave the football hero and his gang. They vow to get even with the chipmunks.
Back at JETT Records, where Ian (David Cross), their former manager worked, Ian is broke, and living in the back room. He blames all his loss on the chipmunks and wants to get back at them someday. A FedEx envelope arrives, and 3 little girl chipmunks chew their way out: Brittany, Jeannette and Eleanor. They want to meet Alvin, Simon and Theodore, and sing with them. Ian lies to the girls, telling them that the chipmunks broke his heart, and got too arrogant, and turned against him, and left him penniless. He hears the girls sing, and realizes he can make a new start with their talent, especially Brittanys.
Back at school, the chipmunks have lunch with the girls, and the football guys are jealous. They come over to give Alvin a hard time, but before they can, the chipmunks give the boys wedgies, which make the girls laugh. Theodore sees a huge bronze eagle statue in the foyer, and runs away, still frightened by eagles. Ryan (Kevin G. Schmidt), the mean football guy, grabs Simon and dunks his head in the toilet, then drops him in. Alvin saves him from drowning, and when they leave the restroom, they see the same boys poking Theodore in the butt and making fun of him, and call him fat. Alvin and Simon attackand end up in the principals office. Principal Rubin (Wendie Malick) tells them they have 2 choices: suspension, or represent the school in a Sing-Off competition. The schools music program is about to be shut down due to budget cuts, so winning the competition and the $25,000 prize would save the program. The chipmunks agree to do it.
Back at home, the boys watch Meerkat Manor together. Toby is busy with his video games and neglects caring for them. They try to tell Toby about their bad day at school, but he just tells them it will be better tomorrow.
First thing at school the next day is P.E., and the chipmunks are getting hit by ball after ball in dodge ball. Alvin, though, challenges Ryan, and catches the ball thrown at him. Ryan talks to him, and says that he has good hands, and they might be able to use him on the football team. Alvin is excitedbut Simon and Theodore are worried. Alvin works out with the football guys in the gym, and starts to become one of them. He even moves to their table at lunch, leaving Simon and Theodore.
Ian sees a notice in the newspaper about the upcoming Sing-Off, and realizes this is his big chance to break the girl chipmunks into the business. He enrolls them in school, and reminds them to avoid Alvin, Simon and Theodore because they cant be trusted.
After school, Alvin, Simon and Theodore are rehearsing, and Ian comes by. He brings the girls, called The Chipettes and has them sing for Principal Rubin. He challenges her decision to have The Chipmunks be the designated singers for the school, so she agrees to a competition Friday night, where applause will decide if its the Chipmunks or the Chipettes to represent the school. When they are at school together the next day, Alvin tries to talk to Brittany, but she snubs him. He tries to warn her about Ian, but she wont believe him.
Ian works the Chipettes hard in preparation for the competition, and comments that Eleanor is too short. He shoves both Eleanor and Jeannette (glasses) towards the back, and says that Brit is going to be a mega-star.
Dave calls and talks to Toby. Toby tells him about Aunt Jackies injury and being in the hospital, and Dave starts to worry. Before he can ask more, Toby hangs up.
The football guys decide to mess with Simon, and tell him hes been selected to be the Litter Monitor. There isnt such a position; they just do it to embarrass Simon. Alvin fins out, but doesnt come to help Simon, as he doesnt want to look bad with his new group of friends. Simon gets angry at Ryan, and he tells him that its a big joke. Simon leaves, mad. Alvin is supposed to play in the big away-game on Friday night and he is excited, but realizes it is at the same time as the competition against the Chipettes.
Helping with Toys for Tots, Theodore and Eleanor meet, and hit it off. She is wearing huge shoes, to make her taller, and stumbles a lot. Theodore tells her she doesnt need them-she is perfect just the way she is. She blushes, and they smile at each other.
At the football game, Alvin is frustrated b/c he hasnt played once. With 9 seconds left and one play, Ryan calls him in, and they run a special Alvin play: Ryan passes the football long, downfield, and Alvin is ON the ball, and when it lands in the end zone, Alvin is on the bottom, and catches it, making a touchdown, and they win. They celebrate afterwards, and Alvin goes with them. Back at the school, the Chipettes sing, and when it is time for the Chipmunks to sings, there is no Alvin. Simon and Theodore go to the podium and explain that without Alvin, they cant sing. They are booed by the students, and the principal proclaims the Chipettes the winner. Alvin shows up much later, when it is all deserted, and realizes his big mistake. He goes home, and is ignored by Simon and Theodore.
In the morning, they find a note from Theodore, saying he has run away form home, and is at the zoo. He has gone to live with the meerkats. He goes through the fence, underneath a sign that says Meerkat Exhibit ClosedBirds of Prey Exhibit Open. Without knowing it, Theodore walks in and faces a large eagle, of which he is deathly afraid. Toby, Alvin and Simon arrive to help him. Alvin distracts the eagle, and then they run for the fence. Theodore gets stuck since he is chubby, and as Alvin pulls, Simon pushes. They make it out in time, and Alvin apologizes for his behavior and they make up.
Ian tells the Chipettes they are opening a concert for Britney Spears, but it is at the same time as the big Sing-Off. He says the Sing-Off never mattered; he just wanted to get them seen so he could make money and be famous again. Ian also says he is only talking Brittany, and when she refuses, he locks all 3 of them in a cage and puts them in a limo. While he is busy, Brittany uses his cell phone and calls Toby, and asks for help. Alvin tries to tell her how to do the lock on the cage. Alvin hops on a motorcycle and tells them he is coming to help.
Pulling alongside the limo, Alvin sees the girls have gotten out of the cage and are on the roof. He throws helmets to each of them, and then they jump down to his motorcycle. They ride off, and Ian is furious. Ian stops and gets a remote controlled helicopter and chases the chipmunks with it. They end up on the skids, hanging on for dear life, and Britney has an idea: they all throw their helmets at Ina, and he drops the remote control. They lean hard to catch it, and Jeannette saves it, and now steers them to the competition. They fly in just as it is their turn, and the audience applauds and cheers. All 6 chipmunks decide to perform together, and they sing,We Are Family, and unanimously win, and save the schools music program. Dave and Toby are in the audience, and cheer.
On the way out, Dave hobbles with Alvin. He has a cast on one leg, uses crutches, and has a neck brace on. Alvin tells him he offered the Chipettes their house and said they could live there with the, Dave looks concerned, and says Alvin!
At the Staples Center for the Britney Spears concert, we see the Chipettes announcedand out come Ian, wearing a gold strapless dress, and with 2 sock puppets on his hands, and one taped to his head. He tries to be the Chipettes, and is booed, and security hauls him offstage.
Back at home, the Chipmunks are in a 3-tiered bunk bed on one side of the room, and the Chipettes are in a 3-tiered bunk bed on the other side of the room. Dave tells them good night, but Alvin refuses to go to bed. Light on, lights off, lights on, lights offDave tries to grab Alvin in the dark, stumbles, a loud crash sounds, and we hear him yell, ALVIN!
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