Yellow Submarine, a 1968 Amination Feature Film

At the beginning of the story, Pepperland is introduced by a narrator as a cheerful music-loving paradise under the sea, protected by Sgt. Pepper's Lonely Hearts Club Band, which falls under a surprise attack by the music-hating Blue Meanies, who seal the band inside a music-proof bubble, turn the Pepperlanders into statues, and drain the countryside of colour.

In the last minute before his own capture, Pepperland's elderly Lord Mayor sends Old Fred, a sailor, (whom the mayor calls "Young Fred") off in the Yellow Submarine to get help. Old Fred travels to Liverpool, where he follows the depressed and aimless Ringo and persuades him to return to Pepperland with him. Ringo collects his "mates" John, George and finally Paul. The five journey back to Pepperland in the yellow submarine, passing through several episodes:

• Sea of Time – where time flows both forwards and backwards to the tune of "When I'm Sixty-Four",
• Sea of Science – where they sing "Only a Northern Song",
• Sea of Monsters – where a monstrous "vacuum cleaner beast" sucks up the entire landscape and then itself, freeing them.
• Sea of Nothing – where they meet a rather helpful "nowhere man" named Jeremy Hilary Boob Ph.D, and sing the song "Nowhere Man" in reference to him. As they leave however Jeremy starts crying and Ringo takes pity on Jeremy and lets him join them aboard the submarine.
• Foothills of the Headlands (or Sea of Heads) – where they are separated from the submarine and John sings "Lucy in the Sky with Diamonds",
• Finally, the Sea of Holes – where Jeremy is kidnapped by one of the Blue Meanies patrolling the outskirts of Pepperland. When Ringo jumps on to a green hole, it turns into the Sea of Green and they arrive in Pepperland.

Reunited with Old Fred and the submarine, they imitate Sgt. Pepper's Lonely Hearts Club Band and "rally the land to rebellion". After singing "Sgt. Pepper's Lonely Hearts Club Band" and "All You Need is Love", Pepperland is restored to colour and flowers re-bloom. The original Sgt. Pepper's Lonely Hearts Club Band are released (thanks to a hole carried in Ringo's pocket from the Sea of Holes) and Ringo rescues Jeremy. The Blue Meanies are forced to retreat, but John extends an offer of friendship, and the Chief Blue Meanie has a change of heart (partly due to some "transformation magic" performed by Jeremy) and accepts. An enormous party ensues, with everyone living happily ever after.

At the end, the real Beatles, having returned home, playfully show off their souvenirs, of which George has the submarine's motor, Paul has "a little 'LOVE'" and Ringo still has half a hole in his pocket (having supposedly given the other half to Jeremy). Looking through a telescope, John announces that "newer and bluer Meanies have been sighted within the vicinity of this theater" and claims there is only one way to go out: "Singing!". The quartet obliges with a short reprise of "All Together Now", which ends with various translations of the song's title appearing in sequence on the screen.