The Hundred Acre Crew and the Digidestined find themselves once again in the realm of Fantasia and discover that there is much more to this musical world than they had imagined. But as they travel through realms such as the Arctic, New York City, and the forest of the Spring Sprite, however, their old enemies, the Masters of Evil and the Crime Empire, are lurking in the shadows, waiting for their chance to strike and get back at them for ruining their plans at Bald Mountain.
- Symphony No. 5 in C minor-I. Allegro con brio by Ludwig van Beethoven. This segment starts without introduction immediately after the opening. Abstract patterns and shapes resemble butterflies in reds, oranges, yellows, greens, blues, purples, and pinks in shades, tints, and hues. Bats explore a world of light and darkness which is ultimately conquered by light.
- Pines of Rome by Ottorino Respighi. A family of humpback whales is able to fly due to a supernova. The calf is separated from his parents when he becomes trapped in an iceberg, but finds his way out with his mother's help. The final section, the Via Appia, gives the impression of the larger pod of adults in migration.
- Rhapsody in Blue by George Gershwin. An episode of New York City in the 1930s in the style of Al Hirschfeld's known cartoons of the time, depicting a day in the lives of four people within the Depression-era bustling metropolis. Featured is an animated cameo appearance of Gershwin himself at the piano.
- Piano Concerto No. 2 in F Major-I. Allegro by Dmitri Shostakovich. Based on "The Steadfast Tin Soldier" by Hans Christian Andersen, the concerto was written as a gift by Shostakovich to his musically gifted young son, and the percussive rhythms also suit a story about a soldier. In contrast to the original story, the ending is a happy one.
- The Carnival of the Animals, Finale by Camille Saint-Saëns. A flock of flamingoes tries to force a slapstick member who enjoys playing with a yo-yo to engage in their "dull" routines. A question in this segment's host sequence leads into its story, "What would happen if you gave a yo-yo to a flock of flamingos?"
- The Sorcerer's Apprentice by Paul Dukas. Based on Goethe's 1797 poem "Der Zauberlehrling", the segment is the only one retained from 1940's Fantasia. Mickey Mouse is the apprentice (of sorcerer Yen Sid) who attempts some of his master's magic tricks before knowing how to control them.
- Pomp and Circumstance – Marches 1, 2, 3 and 4 by Edward Elgar. Based on the story of Noah's Ark from the Book of Genesis starring Donald Duck as first mate to Noah and Daisy Duck as Donald's assistant. Donald musters the animals to the Ark and misses, loses and reunites with Daisy in the process.
- Firebird Suite – 1919 Version by Igor Stravinsky. The story of the spring sprite and her companion, an elk, who accidentally awakes the Firebird, a fiery spirit of destruction in a nearby volcano. The Firebird proceeds in destroying the forest, and seemingly the sprite. The Sprite survives, and the elk encourages her to restore the forest to its normal state.
- The 100 Acre Avatar League (excluding Jean-Bob, Speed, and Puffin), Ash Ketchum, Pikachu, Misty, Brock, Togepi, Littlefoot, Cera, Ducky, Petrie, Spike, Chomper, Ruby, Guido, Grandpa Longneck, Grandma Longneck, Skip, Mr. Thicknose, Simba, Timon, Pumbaa, Genie, The DigiDestined, The Masters of Evil, Dr. Facilier, and The Crime Empire (Joker, Harley Quinn, Two-Face, The Penguin, Negaduck, Megavolt, Quackerjack, Bushroot, and The Liquidator) guest star in this film.
- The Winnie the Pooh series, The Nightmare Before Christmas, Frozen, The Jungle Book, Pinocchio, The Lion King, The Emperor's New Groove, Aladdin, Mighty Ducks, Darkwing Duck, and Fantasia 2000 were all made by Disney.
- Winnie the Pooh: Seasons of Giving, Pokèmon: The First Movie, and Fantasia 2000 were released in 1999.
- The Tigger Movie, Pokémon: The Movie 2000, The Land Before Time VII: The Stone of Cold Fire, Digimon: The Movie, and Fantasia 2000 were released in 2000. The original Fantasia was also released on DVD in this year.
- This is the second time that the Hundred Acre Crew has encountered the Spring Sprite. The first time was in Winnie the Pooh's World of Color.
- When the whole forest was destroyed by the Firebird, this reminds the DigiDestined the destruction of the Twin Tower and lost their families during the 9/11 attack.