As Dave Seville (recovering from an embarrassing fall) finds himself in a French hospital bed, he entrusts his beloved Chipmunks—Alvin, Simon, and Theodore—to his aunt Jackie. At the same time, Ian Hawke, who once reigned as the powerful CEO of JETT Records, now grapples with poverty, leading a life in the basement of his former empire. His fortunes change dramatically when three dazzling female chipmunks, Brittany, Jeanette, and Eleanor—collectively known as the Chipettes—materialize from a FedEx package, captivating everyone's attention.
Back at West Eastman High School, Toby, Jackie's grandson and Dave’s cousin, takes on the responsibility of looking after the Chipmunks. Adjusting to their new environment proves challenging as they face taunts from two envious jocks, Ryan and Xander. The school's principal, Dr. Rubin, a fan who has enjoyed their Denver performances, seizes the moment to engage the Chipmunks in his music program. Ian is left stunned when he sees his former protégés gracing the front page of his newspaper.
As the tension between the Chipmunks and the Chipettes begins to build, Ian smartly leverages their success by enrolling the Chipettes in the same school. The initial encounter between the groups ignites an unforeseen affection, yet Brittany's warning to her Chipette friends—that they cannot trust Ian—hangs in the air like a dark cloud.
Amidst rehearsals, Alvin and his companions struggle to concentrate, their thoughts overtaken by infatuation. Seeing an opportunity, Ian presents the Chipettes to Dr. Rubin, persuading him to let them compete in the upcoming Battle of the Bands. This sets the stage for an inevitable showdown between the two groups.
While Alvin befriends the school's jocks, he inadvertently commits to joining their football team—unaware that it conflicts with the concert. When Theodore and Simon perform at the Battle of the Bands, they are forced to acknowledge Alvin's absence, leading to a default victory for the Chipettes.
Upon arriving at the auditorium, Alvin discovers it empty, only to be met with an impassioned criticism from Brittany for his irresponsibility, leaving him feeling discouraged and uncertain. As he seeks to make amends, Theodore, longing for comfort, escapes to the Los Angeles Zoo, where he finds temporary happiness among a colony of meerkats. But tranquility soon turns chaotic when a fierce wedge-tailed eagle threatens their existence, prompting Alvin and Simon to embark on a daring rescue mission to save their brother from peril.
Meanwhile, the Chipettes face a daunting choice: perform as a supporting act for pop superstar Britney Spears on the same night as the Battle of the Bands or risk being confined in a cage by their ruthless manager, Ian. Tensions escalate as Jeanette and Eleanor are sidelined, compelled to harmonize without receiving due credit. It takes an ultimatum from Britney, who refuses to perform without the full quartet, to compel Ian to allow all four girls their moment in the spotlight.
Just as the Chipmunks seem poised for a solo performance at the Battle of the Bands, a distress call from the trapped Chipettes galvanizes Alvin into action. With Simon guiding him through lock-picking techniques over the phone, Alvin rushes to save his friends. Just in time, they all take to the stage together, delivering a performance that stirs the audience into a frenzy, earning them victory and uplifting their music program.
As the dust settles on this whirlwind day, Dave returns to witness the Chipmunks thriving once again, having joyfully embraced the Chipettes into their family. On a different note, Ian faces an embarrassing downfall at the Staples Centre, where he attempts to impersonate the Chipmunks only to be caught and unceremoniously removed, left to contemplate his fate in a dumpster after the credits roll.
In a lighter subplot, Ryan, Xander, and Jeremy confront the repercussions of their misbehavior, spending a day cleaning gum off the gymnasium bleachers as punishment for bullying the Chipmunks and obstructing Alvin's chance at the sing-off.
