Memories are stored in the form of cards. These cards are used during story events and will dictate the outcome based on how well the challenge is performed. Cards can be earned through story events, purchased at the depot shop, or carried over from previous playthroughs. Collectable objects throughout the map such as mushwood logs, yellow flowers, and xeno eggs can be used during card challenges to change suits, add points, or draw a new hand.

There are five main areas to explore: The Colony Outskirts, Valley of Vertigo, Prosaic Plains, Wresting Ridges, and Subaqueous Swamp. It is not mandatory to venture out of the Colony during a playthrough, though many of the Special Endings require the ability to sneak out and/or explore. Players can find collectables throughout each area, collect cards, and trigger story events that can lead to a wide range of achievements and endings. 

At the start of the game, players are given the decision to choose an augment; a feature that only the player character has and one that will boost different skills. The options include Eagle Eyes, Extra Fingers, Absorbent Brain, Super Strength, Calm Temperament, or nothing. After picking an augment, players are then able to use the rest of the playthrough to hone in on specific skills of their choosing: Empathy, Persuasion, Creativity, Bravery, Reasoning, Organizing, Engineering, Biology, Toughness, Perception, Combat, and Animals. Multiple skills can be focused at once, but trying to boost every skill equally will cause the player to miss out on perks and story opportunities only certain skills can access. 

Throughout the game, players have the ability to form relationships with other characters found throughout the Colony. Character relationships are located in the player menu and are depicted with full or empty hearts, with the value ranging from 0 to 100. Players can pick a character to be their childhood friend at the beginning of the game, which automatically grants a +5 friendship with the character of choice. Childhood friends also give the player certain skill boosts, which can be clues as to what skills to hone if the player wishes to form a relationship with that character. Players grow friendships with characters by bringing them their favorite things, delivering gifts on birthdays, and having conversations.