Pepperland is a vibrant and music-loving paradise beneath the sea, serving as the home for Sgt. Pepper's Lonely Hearts Club Band. The iconic Yellow Submarine is nestled atop an Aztec-like pyramid positioned on a hill, with a stunning backdrop of towering blue mountains.
However, this idyllic land faces an unexpected invasion by the melody-hating Blue Meanies, who originate from beyond the mountains. Their assault begins with a music-proof glass globe, designed to imprison the band members. The Blue Meanies launch projectiles and drop apples (a nod to The Beatles' then-fledgling company, Apple Corps) that turn the inhabitants of Pepperland into immobile statues, stripping the countryside of its vibrant color.
In a desperate final act before his capture, the elderly Lord High Mayor of Pepperland sends Fred on a mission to seek assistance. As the Apple Bonkers comically bonk the Mayor with several oversized apples, Fred departs in the Yellow Submarine. His journey takes him to Liverpool, where he tracks down a downcast Ringo Starr at a location known as "The Pier," which sits atop a hill. With charm and determination, Fred convinces Ringo to join him in returning to Pepperland. Ringo gathers his friends John Lennon, George Harrison, and Paul McCartney in a mission to assist Old Fred, and together they embark on this adventure in the submarine.
Their voyage leads them through the Sea of Nothing, where they encounter a quirky character, Jeremy Hillary Boob Ph.D., who is short and studious. Ringo kindly invites Jeremy to join them on their journey aboard the submarine. They reach the Foothills of the Headlands but inadvertently lose both the submarine and Fred. Subsequently, they find themselves in the Sea of Holes, where Ringo humorously decides to pocket a hole he picks up. Unfortunately, Jeremy is captured by a Blue Meanie, but the group perseveres and makes their way back to Pepperland.
Upon reuniting with Old Fred and restoring the apple-bonked Lord Mayor, they gaze upon the now-dismal, grey landscape of Pepperland. The Beatles don the attire of Sgt. Pepper's Lonely Hearts Club Band and commandeer some instruments. Uniting the residents, they inspire a rebellion against the oppressive Blue Meanies. The Chief Blue Meanie retaliates by unleashing the Dreadful Flying Glove, which John triumphantly overcomes. Color returns to Pepperland as its inhabitants awaken, and flowers begin to bloom once more. Ringo ingeniously uses the hole in his pocket to free the Lonely Hearts Club Band, who join forces with the Beatles to confront the Meanies' multi-headed dog. In a brave act, Ringo rescues Jeremy, who executes "transformation magic" on the Chief Blue Meanie, causing him to bloom roses and reluctantly admit defeat. In an unexpected turn of events, John extends a hand of friendship, leading the Chief Blue Meanie to have a change of heart and accept, revealing he is actually related to the Bluebird of Happiness.
The film concludes with the real beatific Beatles playfully showcasing their souvenirs. George Harrison holds onto the submarine's motor, Paul McCartney possesses "a little 'love'," and Ringo Starr amusingly carries "half a hole" in his pocket, having gifted the other half to Jeremy. As John Lennon peers through a telescope, Paul McCartney inquires about his findings. John responds that "newer and bluer Meanies have been sighted within the vicinity of this theatre," cheerfully claiming, "there is only one way to go out... Singing!" The film wraps up with a lively reprise of "All Together Now," which concludes with translations of the song's title gracefully appearing in various languages across the screen.
