While Dave finds his newest song has gone missing, Theodore finds his pet bird has flown the coop. Dave and the boys hire a shady detective named Private Nose to investigate.

Dave comes home from work to find the yard and the house a mess. Disappointed in the boys lack of personal responsibility, Dave decides to begin acting as a drill sergeant to get The Chipmunks' acts straight.

Dave and The Chipmunks have just completed a very busy schedule and are looking forward to a peaceful cruise. While aboard the ocean liner, Alvin, who only wants to sleep, is constantly being annoyed by an obnoxious social director named Roger Marsell at every turn.

Unwilling to do his chores or to rehearse their new song, Alvin is encouraged by his evil alter-ego to seek out the team's agent and work as a solo act. The evil conscience tells the boy of his future successes without the team.

The Chipmunks are bored so they decide to build a bird house which rather quickly invites an eagle who is nervous to learn to fly. Alvin makes it his personal goal to get him flying.

While vacationing at a beach resort named Surf, Sand & Sea View, Simon, Theodore, and Dave enjoy the scenery as Alvin watches TV, uninterested in the beach. But when Alvin is accidentally hit with a beach-ball by the girl next door, he finds himself head over heels in love.

The boys are tired of being stuck in the house and they convince Dave to take them out by showing him a brochure with beautiful pictures for Valhalla Estates. Dave calls Sam Valiant, now a real estate agent, who tries to sell Dave and the boys a rundown piece of property.

Dave and the boys head for a popular dude ranch out west for a vacation. Once they get to their hotel, they discover that Sam Valiant is the room clerk. Hearing that Dave is trying to write a western song, Valiant keeps pestering Dave to use one of the songs he's written and replace The Chipmunks with himself by using various disguises.

When Dave and the boys go to a national park for their camping trip, they find themselves entangled with a bandit hiding out in the woods.

Alvin meets his new neighbor Bentley Van Rolls III, who turns out to be a spoiled little rich kid. Bentley has his butler, Reese, spy on Alvin from their balcony before heading out to attempt to play with Alvin. Instead of having fun himself, Bentley has his butler play his music and toys for him.

The Chipmunks have just got back home from a long performance tour. While Dave, Simon, and Theodore are cleaning up the house, Alvin tends to his garden only to get into a match with the neighbor's dog who keeps burying its bone in his garden.

The Chipmunks are concerned by Dave's unusual behavior and attempt to follow him. Once they stop in front of the Justice of the Peace, they believe Dave's getting married. Back home they overhear Dave on the phone and believe the woman soon to visit is his fiancé. The boys spy on their conversation and become convinced Dave will get rid of them. When they confront Dave they find out she is really a representative for Sam Sweetheart's Swimming Pools Construction Company who is helping Seville pick out a swimming pool.

While out in the jungles of Africa to record animals sounds for their new record, they hear a new and mysterious sound. While trying to find the source of the sound, Dave discovers are being stalked by a native with what appears to be a deadly blow gun filled with poisoned darts. After they jump into a cauldron and hear "Witch Doctor" playing, they are relieved to hear that the native is not dangerous, but is a fan who wants to play his flute for them.

Theodore finds a dog (Alexander) at an animal shelter and drags him home. Theodore tries to convince Dave to allow a dog to live with them, but he says no since they travel too much. Desperately wanting a dog, Theodore hides Alexander in the basement; when he escapes, Dave believes there are burglars and he calls the police. Dave becomes angry when he finds Theodore's been hiding the dog, but his brothers convince Dave to take him on their trip.

Chuck Wagon, one of Dave's cousins, comes to visit. After he states he can't do anything, Alvin makes it a point to teach him to do everything. hoping something will be his forte.

Alvin tries to play baseball with his team and care for a bratty baby, Billy Brown, at the same time. While Alvin is playing, Billy keeps bugging Alvin to let him play ball, but Alvin won't let him since he is too young. When his team is losing (with the bases loaded), Alvin has the infant play against the rival team's lead player Roger. The little guy, given the nickname "slugger", hits a home run and wins for Alvin's team.

Stanley the Eagle finds a lost necklace and gives it to an eagle statue atop a clock tower. (Stanley thinks that the eagle statue is a female, and he wants to impress her.) Unfortunately for Stanley, the owner of the necklace reports her jewelry stolen and Stanley is being sought by the police. Alvin and his brothers find Stanley and take him to the cops. They drop the charges, but the cops force Dave to be responsible for Stanley.

Dave's ready to rehearse a new song but the boys aren't (Alvin's playing with a yo-yo, Simon's reading, and Theodore's playing with a parakeet (George)). When Dave walks out on his boys (to play golf) following a heated argument about their new song, Alvin takes over and he tries to have his brothers perform a different song. In doing so, he begins to sound like Dave. After some time arguing with each other and the neighbor about how to yell Alvin, a large group of people congregate outside the house. Dave arrives to the pleasure of the boys and they sing his song.

Dave inherits the Chesley Estate and is excited to show the boys. Unknown to Dave, a ghost (JP Lester) is excited to have the opportunity to scare him in order to get the Ghost of the Year award. After the ghost's first failed attempt, Dave has Simon bring the things in from the car and Theodore starts painting while Alvin sets off looking for ghost tracks. The ghost fails three more times at scaring the boys. After failing yet again (mistaken for Alvin), the ghost sleeps with them. In the morning, they find out he is a ghost and take off running. When the ghost accidentally plays a record, he flies away in terror as well.

Daisy Belle comes over to stay at the Seville House while her mother is shopping. When Simon and Theodore take off into another room, Alvin is forced to spend time with her. In order to amuse the girl, he has to use his imagination to create a medieval fantasy. Daisy plays the part of a prisoner held by an evil fire-breathing dragon and Alvin is her brave knight trying to rescue her, but the dragon unfortunately is more cowardly than fierce.

After The Chipmunks disrupt a visit with Mrs. Frumpington by breaking a window and acting sarcastically, Dave loses his temper. Mrs. Frumpington volunteers to teach the boys good manners. She attempts to instruct the boys on how to properly act at the table and how to treat visitors.

Stanley the Eagle attempts to sing with other birds but is driven away. When The Chipmunks find him in his birdhouse, Simon tries to get Stanley to sing for him, but he is too upset. After Dave hears Stanley's failed effort, he tells the boys that eagles can't sing, they scream. Alvin solves the problem by having Stanley play music instead on a pair of cymbals. The boys join in and before long television crews arrive to cover the story.

Dave is out attempting to convince radio stations to play a new track but when he returns he informs the boys they don't want to air singing Chipmunks anymore. Alvin and his brothers set out to save their careers. When a disc jockey named King Malchun still refuses to play the song, "The Alvin Twist", Alvin is determined, sneaking it onto the radio.