The Unterzee has multiple islands, with each island having it's own storylet quests. To progress in the quests, the player has to provide an item or complete a skill check. To acquire the items, the player usually is not able to acquire them at that island and must go to different islands or defeat sea beasts. The skill check takes one of the player's five skills(Hearts, Iron, Pages, Mirrors, and Veils) and based on the value of the skill gives the player a chance to pass the test. Passing the tests often will give the player items, while failing them will occasionally harm the player and will often prevent the player from trying again for a period of time.

One of the main mechanics of the game is horror. As the player travels across the Unterzee he/she will accumulate horror, which has a variety of negative effects.

Each storylet requires the player to either collect items from various places in the Unterzee or to perform various skill checks in order to progress. The player has five skills that affect how well they perform in quests and sailing the Unterzee. These skills are: Hearts, Pages, Mirrors, Veils, and Iron. The heart skill affects skill checks that involve persuasion, health, or reducing terror. Hearts passively reduces the amount of terror the player accumulates while traveling the Unterzee. Pages affects checks involving knowledge, and passively reduces the amount of fragments needed to gain a secret. Mirrors affects checks involving perception, and passively increases the range at which the player can see enemies. Veils affects checks involving stealth, and passively decreases the range at which enemies can see the player. Iron affects checks involving fighting, and it increases the damage your weapons do.