Hibernation

Shelters or hibernation pods are self-sealing chambers the Slugcat uses for hibernation between cycles. Fully resting one of these rooms is the only way to save the game and the best way to progress one's karma level. Resting within one of these rooms is the only way to survive the rain and proceed to the next cycle.

It is likely that shelters are not a real aspect of the Rain World universe, but instead a stand-in for rain-proof areas such as air pockets, since shelters would be much easier to program.

Normal function
The total amount of food required to sleep at shelter is indicated by the food meter at the bottom left corner of the screen, which can be seen when holding the map key. The food necessary to hibernate varies between Slugcat:
 * Monk :
 * Survivor:
 * Hunter :

Entering the square chamber of a shelter with the minimum amount of food will initiate the sealing process and begin the new cycle. Any full food pips to the right of the vertical line aren't necessary to hibernate, and will carry over for the next cycle instead. If the Slugcat is lacking minimum food while entering, the unfilled food pips will flash red, unless the rain is near, in which case you will hibernate anyway, activating starvation mode.

Starvation mode
The Slugcat may force hibernation with one pip or above by holding the down key in a shelter, or entering a shelter when the rain is near. All food will be consumed and the next cycle will begin when you continue. Consequences of hibernating without sufficient food are that the game will not be saved until you reach another shelter with sufficient food, and the Slugcat will enter starvation mode. In this state, the Slugcat will have an ill-color, look skinnier, and will weigh less than a healthy Slugcat.

In starvation mode, the Slugcat will intermittently enter a lethargic state where its eyes close and it will attempt to regain composure similarly to exiting water with very little oxygen left. During these seconds-long periods, the Slugcat moves slower, has weaker jumps and will occasionally cease function for a few moments. During the latter instances, the Slugcat will drop any items it is carrying in its hands.

If you die in starvation mode, everything done in the starvation cycle and everything from the cycle you rested in to begin starvation mode will be lost. In simpler terms, the cycle you died in and the cycle before will not count. If you attempt to sleep with less than sufficient food while already starving, you will simply die.

In order to end starvation mode, the Slugcat must gain a full stomach, including the pips normally in reserve for the next cycle. For Monk, this is five, for Survivor, seven, and for Hunter, nine. This new food requirement will be reflected by a shifting of the vertical line to the end of the food pips. Eating the last pip required suddenly restores the Slugcat's color, size, and stamina.

Alpha
In the alpha of Rain World, the Shelters were seen in two colors: pink, and grey. They had two airlocks on the side along with two entry and exit points. They can be seen closing in the Pup video.

https://www.youtube.com/watch?v=tg3mRF4rqww

Trivia

 * If you enter a shelter with less than sufficient food but have food in the shelter that can satisfy those pips, the shelter will close and you will automatically gain sufficient food at the loss of whatever edible object in your shelter was used.
 * The game only updates progress on achievements when saving or loading in a shelter. If the criteria are met but the Slugcat dies before their next hibernation, their progress is reverted and, depending on the achievement, a penalty may be applied to prevent abuse of the save system.
 * Entering a shelter without any food at all when rain is near causes the Slugcat to be sealed in and starved to death.