A bottlenose dolphin named Ecco witnesses his entire pod vanishing in a catastrophic waterspout while he alone remains behind, sparking a desperate quest to understand what happened. Through conversations with ocean dwellers and guidance from the ancient blue whale known as the Big Blue, Ecco discovers that cyclic storms plague Earth every five centuries—a mystery that leads him to seek out the Asterite, the planet's oldest being. In the sunken ruins of Atlantis, Ecco uncovers an alarming truth: an alien race called the Vortex engineered these storms to harvest Earth's oceans as a food source for their dying world. Armed with newfound knowledge and ancient technology, Ecco travels backward through time to confront the source of the disaster, ultimately gaining the power to fight back and facing the extraterrestrial threat at its origin. His final confrontation with the Vortex Queen becomes the key to rescuing his pod and saving his world from further devastation.