When a group of slugcats is caught off-guard by the rain, the Survivor is flushed into a pit, becoming separated from the others. The Monk is the Survivor's younger brother and jumps after the Survivor. Regardless of which character is chosen, the slugcat wakes up alone to explore the abandoned world. Eventually the slugcat reaches Five Pebbles, a massive, decaying, semi-biotic supercomputer, called an iterator. After climbing up Five Pebbles' leg or exterior, the slugcat falls into the chamber of Five Pebbles' puppet. Five Pebbles explains that, like all creatures, the slugcat is trapped in a cycle of death and rebirth and wants it to end. He then directs it to a place where it can free itself from the "great cycle."
The player is given little explicit guidance and is free to explore the world in any direction by entering pipes and crawling through passages that span across over 1,600 static screens that each spawn their own creatures in set locations. These creatures can then move from freely around the region. The slugcat can jump, swim, and climb poles to avoid enemies while foraging for sparse food, which is used to hibernate in scarce, designated safe rooms called shelters. Hibernating resets the time limit and saves the player's progress. If the player does not reach the shelter before the end of the day cycle, the rain will come, crushing the slugcat or causing them to drown in one of the many now-flooded rooms. Additionally, if the slugcat does not eat sufficient food by the end of the day, the game will not save, and the slugcat will wake up in starvation mode. In starvation mode, the slugcat is much slower, does less damage when throwing spears, and faints if they jump too much. Starvation mode can be exited mid-cycle by completely filling up the hunger bar, but if the slugcat doesn't completely fill up the hunger bar by the end of said cycle, it will starve to death when it tries to hibernate.