When the player starts Exocolonist, they can customize their character, picking traits that affect the rest of the game, like name, gender, and physical presentation, alongside choosing a childhood friend.

The activities include learning about the military, studying in the engineering hub, or exploring the planet outside of the main colony settlement.

After events on Earth led it to be difficult to inhabit, a group of colonists built a ship and set course to a wormhole to take them to Vertumna IV.

Midway through the game, the colony is nearly destroyed by the alien life endemic to Vertumna, and a new militaristic group from Earth arrives to take control on the spaceship Heliopause.

Towards the end of the game, the player has the option of ousting the military governor via coup and stopping the takeover of Vertumna by other colonizers, or letting them remain.

A developer noted that an important part of the early years was making sure "the characters feel natural, and giving you gameplay hooks to hold on to while interacting with them".

The game's focus around giving the player impactful decisions to make was enabled by "thousands of conditional statements" to ensure that it could adapt.