In this sequel, Milo (James Arnold Taylor) has been living quite contentedly in Atlantis studying its fascinating ways. He is reunited with his former crew mates, Mole (Corey Burton), Audrey (Jacqueline Obradors), Vinny (Don Novello), Wilhelmina (Florence Stanley), Sweet (Phil Morris) and Cookie (Steve Barr) by their original benefactor Whitmore (John Mahoney) to solve some puzzling mysteries in the world above. Kida (Cree Summer) believes that many of these occurrences are related the ancient magic - the Crystal- which has protected Atlantis and hidden it. The friends face a horrific sea monster (called a Kraken) which keeps attacking seafaring ships. The sea monster is related to a city where because of a “deal with the devil”made by a town elder everything is miserable and mist-shrouded. The friends also investigate the discovery of ancient artifacts bearing a strong resemblance to Atlantean art. The discoverer has attacked. When the friends see the "attackers" they appear to be wolves and a whirling sandstorm. A Native American shaman tries to counsel the group about the spirits and the sacred resting place of the artifacts before they get too deeply involved. In the end when it is revealed that Atlantean magic had been used in the outside world long ago, Kida must decide whether the power which has hidden Atlantis should be shared with the world.