The movie begins eight thousand years ago with the sinking of Atlantis by a tidal wave accidentally triggered by the Atlanteans themselves. As her people seek shelter, the Atlantean Queen rises into the air and is encircled by a powerful force field which protects the city from the wave. The island then disappears beneath the ocean, leaving nothing behind but a book.
In 1914, Winnie the Pooh, Ash Ketchum and their friends meet Milo James Thatch (Michael J. Fox), an aspiring young linguist working in the boiler room at the Smithsonian Institution in Washington D.C., believes that a manuscript known as the Shepherd's Journal will lead to the location of Atlantis. When his request to lead an expedition is denied by the Institution's board, he finds himself contacted by millionaire Preston B. Whitmore (John Mahoney), a friend of Milo's grandfather. The elder Thatch had already located the Journal, and asked Whitmore to give it to Milo.
Whitmore asks Milo and Pooh and the others to become part of a team with Batman to search for Atlantis on a high-tech submarine. Milo and our heroes joins Commander Rourke (James Garner), his second-in-command Helga Sinclair (Claudia Christian), demolitions expert Vincenzo "Vinny" Santorini (Don Novello), geologist Gaetan "Mole" Molière (Corey Burton), medical officer Dr. Joshua Sweet (Phil Morris), tomboy mechanic Audrey Ramirez (Jacqueline Obradors), cook Jebidiah Allerdyce "Cookie" Farnsworth (Jim Varney), and cynical communications expert Wilhelmina Packard (Florence Stanley).
The sub is sunk by an underwater Leviathan, but the team escapes. After fateful misadventures, they are able to find the underwater entrance to Atlantis. To their amazement, the city still survives in a bubble beneath the earth. They are met by Kida (Cree Summer), daughter of the Atlantean King (Leonard Nimoy). Kida discovers that Milo can read the Atlantean language, long forgotten by her own people. They dive to read ancient underwater murals, and learn about the Heart of Atlantis, which is the source of the power that saved Atlantis from the tidal wave and of the strange blue gems that each Atlanean wears. As they leave the ruins, they are caught by Rourke and the rest of the team, who have turned mercenary and are after the Heart. They find the crystal in a chamber below the King's quarters. Kida is drawn to the crystal and infused with its power.
Rourke plans to take Kida to the surface with the help of the most wanted criminals and villains of Gotham City The Joker, Harley Quinn, Harvey Two-Face and The Penguin. But without the Heart, Atlantis will die. The other team members abandon their plan to steal the Heart, and Rourke leaves them all behind. The King, mortally wounded by Rourke, gives Milo his crystal and begs him to rescue his daughter and save Atlantis. Pooh, Ash, Milo, the others and the Atlanteans discover how to use the crystals to activate ancient flying machines and they give chase as an air force. Rourke plans to escape through an ancient volcano, but the battle causes the volcano to erupt. Milo returns Kida to Altantis barely ahead of the lava flow, and her life force protects the city from destruction just as her mother's once shielded it from the tidal wave.
Milo stays with Kida, determined to restore Atlantis to its former glory. The remainder of the team returns to the surface with Atlantean treasure. For the public, they concoct a tale that they never found Atlantis, and claim that everyone missing had gone down with the sub
- Ash Ketchum, Pikachu, The Joker, Harley Quinn, Two-Face, and The Penguin guest star in this movie.
- This film features the first debut of The Jungle Book Vultures.
- This film is a replacement for Winnie the Pooh Goes to Madagascar which Daniel had to cancel to avoid getting suspended by DreamWorks SKG.
- The Winnie the Pooh films, The Jungle Book, and Atlantis: The Lost Empire were created by Disney.
- Both Pokémon 3: The Movie and Atlantis: The Lost Empire were released in 2001.
- The Storyline continues in Winnie the Pooh Goes to Atlantis II: Milo's Return.
- Winnie the Pooh Goes to Atlantis: The Lost Empire Part 1: https://docs.google.com/file/d/0B35Ri2vUrFXpUXdDNDZlN3BPVDA/edit
- Winnie the Pooh Goes to Atlantis: The Lost Empire Part 2: https://docs.google.com/file/d/0B35Ri2vUrFXpMkZ3ZkNhTE9VU0k/edit
- Winnie the Pooh Goes to Atlantis: The Lost Empire Part 3: https://docs.google.com/file/d/0B35Ri2vUrFXpeU8xNjgzdXRLTU0/edit
- Winnie the Pooh Goes to Atlantis: The Lost Empire Part 4: https://docs.google.com/file/d/0B35Ri2vUrFXpdVp0a0lDVmdZOFk/edit
- Winnie the Pooh Goes to Atlantis: The Lost Empire Part 5: https://www.dropbox.com/s/1tveluw7eyszvtc/Winnie%20the%20Pooh%20Goes%20to%20Atlantis%20Part%205.wmv?dl=0
- Winnie the Pooh Goes to Atlantis: The Lost Empire Part 6: https://docs.google.com/file/d/0B35Ri2vUrFXpd2hQYmVWZ2RKX1E/edit
- Winnie the Pooh Goes to Atlantis: The Lost Empire Part 7: https://docs.google.com/file/d/0B35Ri2vUrFXpUTZpZnFzYW0yQWs/edit
- Winnie the Pooh Goes to Atlantis: The Lost Empire Part 8: https://docs.google.com/file/d/0B35Ri2vUrFXpbEhHUnc1djlWY1U/edit
- Winnie the Pooh Goes to Atlantis: The Lost Empire Part 9: https://docs.google.com/file/d/0B35Ri2vUrFXpZWE1NnlZVFRfc0U/edit
- Winnie the Pooh Goes to Atlantis: The Lost Empire Part 10/Credits: https://docs.google.com/file/d/0B35Ri2vUrFXpdFRrQVJqdzJLa28/edit