Plot

The Plot (SPOILERS!)
You play as a young slugcat separated from your family during one of the periodic heavy rains and floods on his world. You are now on your own to survive and find food. (The opening cinematic screens show a few plants and creatures the slugcats eat, providing a few hints as to gameplay, but the player is left to figure out hibernation and the symbol system more or less on their own.)

Mysterious guide
Shortly after becoming separated, you find a yellow creature that seems to act as your guide. To begin with, the 'guide' points you towards food and safe places to hibernate. As you progress, the guide starts showing you octagonal holograms of strange creatures.

Looks to the Moon
As you progress through a region called Shoreline, the guide's hints at direction become more urgent. By following them, you eventually find one of the creatures from the holograms, alive and seemingly imprisoned. Later in the game it's possible to discover that this creature is named Moon.

At this point there are at least two possible choices. Moon is surrounded by glowing flies ('neurons') that you can easily pluck out of the air, but if you do, Moon seems to beg you not to. You are able to press ahead despite Moon's wishes and eat the neurons, which seems to hurt Moon. Eating all of them renders Moon unresponsive, possibly dead.

If you eat one or more neurons, you acquire a permanent glow referred to in achievements and by developers as 'enlightenment'. Your next hibernation will show a dream about Moon seemingly begging for mercy. Your guide abandons you immediately if you harm Moon in this way, and your only hints from then on are glowing symbols that point you in the right direction when touched.

If you do not eat any neurons, but instead leave peacefully, on your next hibernation you will dream about sitting and talking with Moon. At this point, or later, you can complete an optional subquest (below).

Returning at least one neuron to Moon grants you the 'enlightenment' power in a non-harmful way.

After this point you'll also begin to see occasional blue guide creatures (possibly associated with Moon, as the orange guides could be associated with a later character). The blue guides don't seem to provide any actual guidance.

Darkness and Pebbles
Once you have the enlightenment power from either method, or possibly without it, you continue your journey and eventually find yourself inside a giant semi-organic computer named Five Pebbles. When you reach a central area, you meet a second creature like Moon, who seems to be the 'brain' or communicative component of the entire machine. Five Pebbles tells you some significant lore and shows you the way out. A tiny square icon that appears above your head will allow you into this route.

If you return to Moon after this, you will be able to communicate with her too.

Pearls for Moon
After talking to Five Pebbles, if you return to Moon, she will recognise that you can now understand her. Moon has a missing neuron, which you are able to find and return to her, to her relief.

Moon's long-term memory storage is severely damaged as a result of some past events that you can learn about by finding special coloured pearls, which are forms of data storage, and bringing them to her to read.

This optional side quest reveals significant lore about the world and long-ago events (major spoilers!).

Escaping the cycle
Following Five Pebbles's directions, you are sent west through an area called Farm Arrays, and eventually deep down into the earth. You pass through ancient temples Pebbles mentioned and continue further downwards, passing through strange fluid whose nature is a mystery unless you have completed parts of Moon's side quest.

Ending
The ending shows you transcending the cycle of life and death, apparently reaching enlightenment and nirvana. It is bittersweet, however, because you are not reunited with your family (and may never be, unless they someday take the same path you did).