Ash Ketchum and his friends have traveled to the Antartica and met a Penguin named Hubie who finds a special pebble for his future mate, Marina, gets thrown out to the sea by an evil Penguin named Drake (whom The Crime Empire, Team Rocket, Sharptooth, Ozzy, Strut, Ichy, Dil, Rinkus Sierra, Red Claw, Screech, Thud, Carface, Killer, Oogie Boogie, Warren T. Rat, and Cat R. Waul work for), and meets another Penguin named Rocko. Together they must head back to the Antartica and save Marina.
- Littlefoot, Cera, Ducky, Petrie, Spike, Chomper, Ruby, Guido, Grandpa Longneck, Grandma Longneck, Skip, Mr. Thicknose, Rex, Woog, Elsa, Dweeb, Roger Rabbit, Taran, Princess Eilonwy, Fflewddur Fflam, Gurgi, Scooby-Doo, Shaggy Rogers, Fred Jones, Daphne Blake, Velma Dinkley, Scrappy-Doo, Jack Skellington, Zero, Aladar, Neera, Plio, Yar, Zini, Suri, Baylene, Eema, Url, Fievel Mousekewitz, Tiger, Tony Toponi, Tanya Mousekewitz, Yasha Mousekewitz, Papa Mousekewitz, Mama Mousekewitz, Charlie Barkin, Itchy Itchiford, The Crime Empire (Joker, Harley Quinn, Two-Face, The Penguin, Negaduck, Megavolt, Quackerjack, Bushroot, and The Liquidator), Team Rocket (Jessie, James, and Meowth), Sharptooth, Ozzy and Strut, Ichy and Dil, Rinkus and Sierra, Red Claw, Screech and Thud, Carface, Killer, Oogie Boogie, Warren T. Rat, and Cat R. Waul will guest star in this film.
- This is an NTSC film with NTSC bits from the Pokémon films, The Land Before Time films, We're Back! A Dinosaur's Story, Who Framed Roger Rabbit, the Roger Rabbit shorts, The Black Cauldron, the Scooby-Doo films, The Nightmare Before Christmas, Dinosaur, An American Tail films, the All Dogs Go to Heaven films, and Batman: Mask of the Phantasm.
- Warner Bros. Family Entertainment (the studio that released the first three Pokémon films and Batman: Mask of the Phantasm) released The Pebble and The Penguin outside the US.
- The Land Before Time, An American Tail, All Dogs Go to Heaven, and The Pebble and the Penguin were all created by Don Bluth.
- Yru17 originally planned to re-edit a separate Land Before Time crossover with The Pebble and the Penguin, but he retired from re-editing anymore crossovers, so Littlefoot and his friends ended up guest starring in this film instead.
- Littlefoot, Cera, Ducky, Petrie, and Spike have faced Drake before in the Disneyland version of Winnie the Pooh in Fantasmic!. However, this film will mark the first time Chomper, Ruby, Guido, Littlefoot's grandparents, Skip, and Mr. Thicknose will face Drake.