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 Warrior 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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