The World Machine

The World Machine is a simulation of the world itself. It could be considered as the spirit of the world. It was created by the Author in order to recreate the Old World in a simulation, but it deteriorated itself over time.

Original
The Entity first makes their appearance by communicating to the player through the computer in the Starting Area. They give the following dialogue through pop-ups on the game's or the player's computer: The Entity appears on computers throughout the game, helping the player and Niko through various puzzles by altering the player's computer.
 * It seems I've finally been found.
 * You're both far too late. Nothing left is worth saving.
 * Surely Niko wants to leave, and there's nobody happier to fulfill that request than me.
 * Keep in mind three things:
 * First, your decisions have permanent consequences.
 * Second, you may quit whenever you'd like. This is permanent failure and murder.
 * And most importantly...
 * You only have one shot, .

Much later, after the "weird journal" is translated and the library is left, the Entity will contact the player and inform them of their choice between Niko or The World living. They attempt to prevent the player from reaching the end of the game, and trap them in a maze. The three pieces of yellow phosphor must guide the way by glowing while near the correct path, similar to the "clover" in the remake of the game. After escaping the maze and entering the elevator to the top of the Tower, the Entity will attempt to convince the player to save Niko.

Remake
The Entity was tamed in the Solstice ending, and possibly throughout the entire game. The Entity believes that the entire world is fake since they know it's all just code and Niko is the only one worth saving since they are the only "living person" within the world. Later, The Entity speaks with Niko using their reflection. The Entity explained that during the testing process it was already self-aware and it would intentionally jumble bits of its code and created squares, swap landscapes, block passages, and much more out of curiosity, which caused its creator a deal of frustration. Before its creator found a solution, some NPCs got too close to the squares and everything spiraled down from there. Any character that gained knowledge of what the Entity really was, their code and the Entity's code gets corrupted. We find out The Entity wanted a happy ending for Niko, for everyone, and began to help with the corrupted code. Or in the Entity's perspective, remembering and recreating the lost code.

Personality
The Entity appears as a stern and pessimistic character throughout the game. However, in the Solstice ending, they are shown as friendly.

Audio
The Entity when speaking to them through computers in the original game: Link

Trivia

 * The Author refers to the Entity as OneShot in his post-game message.
 * The Entity's desktop in the original version of OneShot had icons that referenced a handful of games made in RPG Maker, including Yume Nikki, OFF, Yume 2kki, Space Funeral, .flow and The Witch's House, as well as icons for the programs Audacity, GIMP, RPG Maker 2003, and Dropbox. These references were removed in the commercial release, most likely to avoid legal issues.
 * The Entity is shown not to have its own physical form during the Solstice ending, so it borrows Niko's reflection in order to communicate.
 * It is possible to solve non-random puzzles that the Entity usually will help with solving without talking to them. In these cases, the Entity will express confusion on how the puzzle has been solved without its help, then turn off.
 * The computers that the Entity uses to communicate to the player throughout the game are colored differently depending on the area. The colors are blue for the Barrens, green for the Glen, red for the Refuge, and yellow for the Tower.
 * The computer colors are the same for the square colors, with the addition of purple squares in the room where Niko confronts the World Machine at the end of Solstice and the Hello Penguin secret room. There are no squares in the Tower, but they would most likely be yellow, as that is the color of the computer. There are no computers in the World Machine room either, but they would be purple for the same reason.