The game opens with Ecco, a bottlenose dolphin, as he and his pod are swimming in their home bay. A podmate challenges Ecco to a game to see how high he can jump into the air. When he is in the air, a giant waterspout forms and sucks up all marine life in the bay except Ecco, leaving him alone in the bay. Upon leaving the bay, Ecco swims around meeting other marine life including other dolphins who tell them they have felt the storm and the entire ocean is in chaos. An orca Ecco encounters tells him to travel to the Arctic to meet the "Big Blue," an old blue whale revered by marine life for its age and wisdom, who might be able to help him on his journey. Arriving in the Arctic after a long travel through the ocean, Ecco finds the Big Blue who informs the dolphin the storms occur every 500 years. Though the Big Blue doesn't know what causes the storms, he suggests Ecco find the Asterite, the oldest life form on Earth. He leaves the Arctic and travels to a deep cavern where he finds the Asterite. The Asterite greets Ecco telling him though it has the power to aid him, the Asterite cannot because orbs from its body have been lost. The Asterite tells him to go to the sunken ruins of the city of Atlantis, and use the time machine left behind by the Atlanteans.
Ecco travels to the sunken city of Atlantis, where he discovers an ancient library filled with Glyphs, giant crystals stored with information. From the library Ecco learns the origins of the storms, an alien race known as the Vortex lost the ability to produce food on their planet, so every 500 years when the planets align, they use their technology to harvest the waters of Earth. The Atlanteans fought a long war with the Vortex that ended when a beam struck Atlantis from space sending the city into the depths of the ocean. Learning this, he activates the time machine and travels 55 million years into Earth's past. While Ecco is in the past he learns an ancient song to communicate with a Pteranodon. Ecco locates the Asterite in the past but is immediately attacked by it. Forced into battle, he manages to dislodge a globe from it. This opens a time portal and he is sent back into the present. After receiving the globe, the Asterite grants him the power to turn his sonar into a deadly weapon against the Vortex, as well as the abilities to breathe underwater and to slowly regenerate lost health. The Asterite instructs him to use the time machine to travel back in time to the hour of the harvest. This time he manages to be sucked into the waterspout with his pod. Ecco is sent flying through outer space to a giant tube-like machine. Making his way through the construct Ecco arrives on the planet Vortex engaging the aliens in combat. He makes his way to the Vortex Queen and engages her in a fight. When the Queen is defeated she spits out Ecco's pod she ate and they make their quick escape back to Earth.
