This is the official Storyline for Ecco - The Tides of Time taken from the manual of the Genesis Version.
Reading this will spoil Ecco 1 for you if you don't know it yet, so be warned!
The waters of Home Bay swell with the deep blue of peace. Ecco swims and frolics in the surf. The sea is warm, calm and full of good fish
Best if all, Ecco's pod is with him, safe again. In fact, it's Ecco who's making waves, leaping, twisting and joyously jumping, challenging his podmates to races and feeding contests!
The Vortex now seems so far away. The Vortex the nearly invincible, secret, yet supremely dangerous enemy. It's only beena short time since this monster, in a churning whirlpool, tore Ecco's family from Home Bay. Then Ecco braved the terrors of unknown waters to find and defeat this evil menace that fed on the creatures of the sea.
His adventure had taken Ecco through deadly hazards, from the rip tides of southern gulfs to the frozen chill of northern seas. Ecco had fought paralyzing sea worms, giant Arctic spiders, trilobites and other strange beings. He had sought help from mysterious - sometimes awesome - denizens of the deep, like his friend Big Blue, the Great Blue Whale.
In his quest, Ecco had discovered the Asterite, a mystical, benevolent creature of great wisdom who had given Ecco strong powers. He had encountered the Atlanteans in their sunken city, and with their help, travelled back in time 55 million years. He had even voyaged to another planet light years from Earth! He had fought the Vortex, and he had saved his family!
Although his quest is over, Ecco still enjoys the powers bestowed upon him by the Asterite. He can breathe underwater without having to find air pockets. His song can become a formidable blast of sound. He is stronger and faster than before.
As Ecco sports with his family, he leaps high into the air, and plunges to the bottom of the shallow lagoon. He is unaware of a new danger that lurks in the seabed - one he led back to Earth...
...The Vortex Queen, though weakened, was not destroyed. She followed Ecco from her hive in deep space back to this new, nourishing planet. Now, plunging into the warm waters of Earth, she seeks out a deep chasm ad sinks into the abyss. Here she can feed upon the Earth as she spawns stream after stream of Vortex young.
Her feeding builds in strenght, creating a downward current against which small fish struggle in vain. She is creating a new Vortex race, and her presence on Earth bodes doom for all its creatures!
Ecco must rid world of this engulfing evil. Even as he tumbles in the waves, the future is unfolding. But must it be a dark future ruled by the Vortex, lifeless, miserable and cold? Does Earth have any chance of a warm future, teeming with energetic life?
Ecco must stop the Vortex! He is "the stone that splits the stream of time." He now faces a quest far more dangerous than any he's yet undertaken. For Ecco must save not only his dolphin pod, but the Earth and all living beings!