Originally, Disney was developing a sequel entitled Shards of Chaos, but it was abandoned once The Lost Empire was less successful than anticipated. The released sequel consists of three animated shorts, originally meant to be three episodes of a series that was never completed called Team Atlantis. Some additional animation was done to link the stories more closely.
After the decline in Atlantean culture following the sinking, Kida, now Queen, and married to Milo Thatch, is using the heart of Atlantis to restore her city's former glory. Suddenly, Milo's comrades and Mr. Whitmore arrive in Atlantis; while their arrival is unexpected, the Atlanteans welcome their old friends. Unfortunately, they have come to inform them of mysterious creature causing trouble on the surface. They arrive in Norway and discover that the mysterious problem is actually the creature known as the Kraken, which had been attacking shipping freighters and taking their cargo to a cliffside village. At first they presume it to be an ancient Atlantean war machine gone rogue (like the Leviathan from the previous film), but they discover that the town magistrate, Edgar Volgud, seems to be controlling the Kraken. They soon learn, though, that the Kraken itself is the master, having made a deal with Volgud. When they blow up the Kraken, the man disintegrates and restores the spirit of the village.
All the while, Kida is learning about the outside world and is adapting well. However, she still feels guilty, as there could still be other Atlantean war machines in the world causing problems, like the Leviathan. Their next mystery is in the Southwestern United States, involving coyote spirits opposing them. They later find a hidden city in Arizona that contains a statue that greatly resembles Atlantean architecture. Unfortunately, a very sly shop owner, Ashton Carnaby, intends to pillage the place for its valuables, but the spirits then turn him into one of them. A Native American man named Chakashi, who is a Native American wind spirit, trusts them with the knowledge of their sanctuary and informs Kida that she can choose Atlantis' destiny.
Returning home, the adventurers discover that one of Whitmore's old competitors Erik Hellstrom, believing himself to be the Norse god Odin, stole one of his possessions, an ancient spear called the Gungnir, presumably an artifact of Atlantean origin. When they track him down in the frigid Nordic Mountains, he presumes Kida to be his long lost daughter and kidnaps her. His intentions are to end the world in Ragnarok. He creates a lava beast and then an ice beast to destroy the world, but well-placed explosives used by Vinnie distract the monsters long enough for Kida to retrieve the spear and vanquish the beasts. During these escapades, Kida comes into a greater understanding of just how powerful the Atlantean Crystal is, and that she must choose between hiding it and sharing it with the rest of mankind.
Having retrieved the spear, Kida realizes her father was wrong to hide the Crystal from mankind. She combines the Spear with the Heart Crystal and lifts Atlantis to the surface. Two fishermen are shocked when they suddenly see an entire continent rise before them. In the end, we see Atlantis above the water for the first time in over nine-thousand years. Mr. Whitmore narrates that from then on, the world was a better place.
- James Arnold Taylor - as King Milo James Thatch
- Cree Summer - as Queen Kidagakash "Kida" Thatch
- John Mahoney - as Preston B. Whitmore
- Jacqueline Obradors - as Audrey Rocio Ramirez/Nurse
- Don Novello - as Vincenzo "Vinny" Santorini
- Corey Burton - as Gaëtan "Mole" Molière
- Phil Morris - as Dr. Joshua Strongbear Sweet
- Florence Stanley - as Wilhelmina Bertha Packard
- Frank Welker - as Obby/Mantell
- Steve Barr - as Jebidiah Allerdyce "Cookie" Farnsworth
- Clancy Brown - as Edgar Volgud
- Jean Gilpin - as Inger Eliassen
- Kai Rune Larson - as Seaman/Gunnar
- Bill Fagerbakke - as Sven
- Thomas F. Wilson - as Ashton Carnaby
- Floyd Red Crow Westerman - as Chakashi
- Jeff Bennett - as Sam McKeane
- W. Morgan Sheppard - as Erik Hellstrom