Plot

The basic plot of Rain World is described in this article, describing the path a new player is most likely to take. Deeper lore exists within the game, but is much harder to find.

The Plot (SPOILERS!)
You play as a slugcat, a nomadic, omnivorous creature who relies on a small herd community, intelligence, and the use of simple thrown tools to thrive in a world filled with predators and periodic torrential rains. As a deadly storm approaches, the slugcat stumbles during a climb and is separated from its family. Left alone, it must struggle to survive, and eventually thrive, in a dangerous and unforgiving world.

Mysterious guide
Shortly after starting the game, the player encounters a strange yellow creature who takes an interest in the slugcat, acting as its guide for reasons unknown. The creature will help the slugcat survive by pointing out food and shelter when needed, as well as alerting the player to threats. As some time goes on, the creature will begin guiding the player along a given path, showing symbols and pictures which indicate you are heading towards the slugcat's lost family...

As the slugcat's journey goes on, it will encounter a variety of strange creatures, including other sentient life in the form of scavengers. The guide helps the slugcat deal with these creatures. As the journey continues, the guide stops indicating the presence of the slugcat's family, and begins urgently directing the slugcat to a strange humanoid being...

Looks to the Moon
Far out in the shoreline, the player eventually finds a vast mechanical complex in shambles, and the guide directs the slugcat inside of it, indicating that the being within may be able to assist it. Within the complex, the player eventually finds a seemingly helpless blue robotic creature in a heavily damaged central chamber, which it may later discover is Looks to the Moon. However, she is unable to communicate with the player through anything more than incomprehensible chirping, and offers no apparent help. Several small flying creatures circling moon may catch the player's eye, however, offering the player another course of action...

A New Friend
Should the player opt to ignore the neuron flies, the guide will suddenly beckon the player upwards towards a new destination. The guide will indicate the desire for the slugcat to return with additional neuron flies for Moon, who is suffering from a lack of processing power and memory. Such is Moon's deterioration that she won't even remember the slugcat's visit until something more eventful happens.

Stolen Enlightenment
If the player grabs hold of a Neuron Fly, Moon will panic and try to get the slugcat to drop it. Should the player eat a neuron fly, Moon will cry out in distress and writhe in agony, apparently seriously damaged by this. Slugcat will begin glowing, however, gaining a trait referred to as 'enlightenment'. This will help the player get through certain areas of the game, but the guide will take the slugcat's betrayal very seriously, reacting angrily and leaving the slugcat by itself. Curious orange spirits will be the player's only guide upwards, towards a new unknown structure...

Five Pebbles
Journeying upwards will lead the player to scale and eventually enter a sprawling compound filled with unusual threats. The structure appears similar to Moon's, but in a much less damaged state. At the heart of this compound lies another iterator, Five Pebbles. Upon entering this chamber, Five Pebbles examines the player, briefly attempts to communicate, and then proceeds to insert a chip into the slugcat's brain, granting the player the gift of communication. He infers the slugcat wishes to escape the cycle of reincarnation it is stuck in, and directs it towards a spot deep in the earth, where it can free itself from the cycle.

Returning to Moon and Stealing Neurons
With the gift of communication, the player is able to return to Moon and communicate with her. Moon has much to say, but will not be very friendly if the slugcat ate any of her neurons. If the player follows the advice of their guide and steals neurons from Five Pebbles to return to Moon, she will be thankful, and may even forgive the slugcat if it had eaten a neuron previously. Bringing neurons restores some of Moon's memories and abilities, and she will be able to read pearls you bring her, giving the player much more insight into the history and lore of the world.

Ending
When the player reaches the depths, it will discover a temple guarded by strange beings. Thanks to either the mark given by Five Pebbles or the blessings of the Echos, which bestow a higher potential for Karma, they will let slugcat pass without trouble. Deep within the temple lies a lake of void fluid into which the player must dive. After diving for some time, a godlike being assists the slugcat in ascending. Its old life gone, the slugcat seems to reunite with the souls of many other slugcats, perhaps including its family. It is important to note that some time after meeting the other slugcats a white light appears, which the player must swim to in order to finish the game.