The game begins with Ecco as he and his pod are swimming in their home bay. One podmate challenges him to see how high into the air he can jump. When he is in the air, a waterspout storm forms and sucks up all marine life in the bay except Ecco, leaving him alone in the bay. Upon leaving the bay to search for his pod, he contacts several dolphins from other pods, who tell him the entire sea is in chaos, and that all marine creatures had felt the storm. After talking to an orca, Ecco travels to the Arctic to find ablue whale named The Big Blue. The Big Blue tells him such storms had been occurring every 500 years and directs him to the Asterite, the oldest creature on Earth. He leaves the Arctic and travels to a deep cavern where he finds the Asterite. Although it has the power to aid him, one of its globes is missing, and needs it returned. However, this can only be achieved by traveling back in time using a machine built by the ancient Atlanteans.