The underwater volcanoes turn out to reveal a clue to the legendary underwater city of Atlantis. A small group goes exploring and finds what appears to be an ancient outpost of the lost civilization, but also realizes that it is home to terrifying sea lilies and the crew must fight for their lives.

When it is revealed that Nemo has been too daring and put the crew in danger, they lock him in his cabin and Boniface takes command instead. At the magnetic north pole, the problems pile up. Nemo must unite his divided crew by telling them who he really is.