In Aquanaut's Holiday: Kakusareta Kiroku, the player boards a subway and explores the deep ocean around an fictional atoll. In contrast to the predecessors, the game tells a story about a research station and centers around their employees Jessica Porter and Robert Kemelmann; the player takes the role of a journalist in search of a missing researcher. The story is told through dialogue, mostly serves to unlock new and varied areas to explore and later takes a slightly futuristic turn.
Despite the story, the main drive of the game is still to explore the ocean and its species as end in itself. In order to solve the story missions, the player needs to explore in order to find specific places (e.g. mysterious stones) and to find sonar buoys. Those have to activated with batteries in order to improve the submarine's range of operation and unlock new areas. The batteries have to be bought at the research base with money rewarded for discovering new creatures. Also available for purchase are special buoys which can be deployed as fast-travel points (the player can always jump to the research base).
The only typical game feature are special fish (three per area) which can be located by following their sound. After approaching them, the player has to solve a Simon Says mini game (which becomes harder after each fish) and is rewarded with red slime. This slime is used to upgrade the submarine's speed, agility, battery/buoy capacity or unlock the ability to make photos. Otherwise the submarine has no influence to its surroundings - it is invisible to sea creatures and it is impossible to crash against the environment. The game also has a in-game encyclopedia of all areas and creatures the player encounters.