In Endless Ocean, the player plays as a scuba diver exploring the Manaurai sea,[Note 1] a fictional sea in the South Pacific, in search of sea life and sunken treasure[7] under the guidance of their assistant, Katherine Sunday.[8] In the sea, they will encounter several marine species, ranging from smaller fish and penguins to whale sharks, manta rays and sperm whales, as well as dolphins and other cetaceans that can be trained to perform certain behaviors and become companions. Species such as sharks are also present; however, they pose no threat to the player. The player also has access to a large aquarium, which they can populate with species they have identified. The sea's various locations provide a means for the player to experience diving, cave diving, deep-water trench exploration, wreck diving, and other activities that might not otherwise be possible in a single real-world setting.
Late in the game, Katherine tells the player that in the past, her father set out in search of a unique whale called the White Mother, but never returned. The player and Katherine set out to find the White Mother, which entails seeking out the four types of whales present in the game, humpback whale, North Atlantic right whale, sperm whale, and blue whale, and placing motion sensors on different points of the map. Eventually, one of the sensors is set off, and the player witnesses the White Mother, a large albino blue whale, as Katherine remembers her father.