Pepperland, an idyllic, music-loving paradise under the sea, is suddenly attacked by the Blue Meanies, a group of music-hating creatures who aim to silence all joy and color. Captain Fred, a sailor from Pepperland, escapes the oppression in a yellow submarine. He travels to Liverpool, where he seeks help from the Beatles. The band—comprised of John, Paul, George, and Ringo—agree to join Fred on his mission to save Pepperland. They embark on a fantastical journey through various dreamlike and surreal landscapes, encountering bizarre characters and challenges along the way.

As they voyage through surreal seas, encountering places like the Sea of Time and Sea of Nothing, the Beatles use their camaraderie and musical talents to overcome obstacles and gain allies. Each stop along their route brings new visual marvels and sonic experiences, capturing the spirit of 1960s psychedelia. Eventually, they arrive in Pepperland, finding it oppressed by the Blue Meanies. Here, the Beatles’ music becomes a powerful tool against tyranny, symbolizing the triumph of art and love over oppression.