The world's most highly qualified crew of archaeologists and explorers is led by historian Milo Thatch as they board the incredible 1,000-foot submarine Ulysses and head deep into the mysteries of the sea. The underwater expedition takes an unexpected turn when the team's mission must switch from exploring Atlantis to protecting it.

Milo and Kida reunite with their friends to investigate strange occurances around the world that seem to have links to the secrets of Atlantis.