In the future, the ocean has developed its own mind and is connected across the planet by waterways traveling through the sky. She is his descendant, Trellia, who takes him to the distant future to speak with 'an old friend'. Soon after, Ecco meets a dolphin with unusually long fins. His fellow dolphins explain that something has killed the Asterite and is now spreading fear among the ocean life. As Ecco recovers, he discovers that the Asterite's powers have left him (indicated by the return of his need to surface for air).

One day, while Ecco is out exploring an underwater cave, a powerful earthquake goes off and causes an avalanche. Still wielding the powers granted to him by the ancient life-form known as the Asterite, Ecco has since returned to his peaceful life in Earth's waters. The Tides of Time continues from the ending of the original game, in which Ecco had saved his dolphin pod and the Earth from the Vortex aliens. The player is forced to restart if Ecco misses too many rings or takes too much damage.

In these stages, Ecco must swim through moving rings while avoiding or attacking enemies. The transformations are level-specific and include a seagull, a jellyfish, a shark, a school of fish, and a Vortex drone. The second is the 'Metasphere', which transforms Ecco into different animals. The first is the 'Pulsar', which grants Ecco the ability to fire a multi-directional sonar attack at enemies for the duration of the stage. New puzzles include following other dolphins through an underwater maze and a 'scavenger hunt' in which Ecco must collect the Asterite's missing globes.

As a mammal, Ecco is also required to surface for air at regular intervals. By combining his charge and sonar, Ecco can attack enemies from a distance. Ecco's main attack is to ram into enemies at high speeds, while his sonar is used to communicate with other cetaceans and interact with certain objects such as crystal Glyphs, as well as bring up a map of the area through echolocation. The Tides of Time maintains the same gameplay as its predecessor.

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