Development of what might have been the game began shortly after the release of Drakengard 2 with the decision to make the game for the PlayStation 3 fueled by the console's recent release and the belief that releasing the game on the PlayStaiton 2 would put the game at a disadvantage. However, the original ideas were reworked, and eventually the project became a spin-off titled Nier.
After Nier was released and the company that made it, Cavia, was disbanded, Takamasa Shiba and Yoko resurrected plans to create a proper next entry in the series. As part of the brainstorming process, the company used fan questionnaires from which the team learned that fans wanted a dark story similar to Nier for the next entry in the series. During the process, the team decided upon a female protagonist as the game's lead, in contrast to the previous games which had featured male protagonists. Many aspects of Zero's design and abilities were intended to evoke the game's gritty atmosphere, while the flower growing from her eye was almost cut when Shiba thought it would be too much of a risk for the series when coupled with the character's gender.