In Atlantis: The Lost Empire, Milo Thatch is a linguist and historian who believes that the legendary underwater city of Atlantis is real and seeks funding from a wealthy benefactor to explore it. He manages to convince a team of experts to join him on the expedition, including a mechanic named Vinny, a doctor named Sweet, a demolitions expert named Audrey, and a geologist named Moliere.
Together, they board the Ulysses, a state-of-the-art submarine designed by eccentric inventor and military commander, Commander Rourke. The team reaches Atlantis and discovers a beautiful city ruled by Princess Kida, who possesses the power of a magical crystal that keeps the city's inhabitants alive.
However, their mission to explore the city and learn its secrets takes a dangerous turn when Commander Rourke and his mercenaries betray the team and attempt to steal the crystal for their own gain. Milo and his team must band together to protect Atlantis and its people from destruction.
Throughout the film, the team battles various obstacles and confronts personal challenges as they uncover the mysteries of the lost civilization. Along the way, they discover that the fate of Atlantis is tied to their own, and they must make difficult choices to save the city and themselves.