The Marionette Project is an experiment underpinning the plot of Kagero: Deception II. Overseen by the Timenoid Yocal, the goal of the project is to raise a human to serve as an unquestioning hunter of other humans. The only known test subject of the project is Millennia.

As a result of the project, Millennia is a young woman of no emotion that kills humans without question or mercy. The ultimate success of the project is arguable, as Millennia's fate varies depending on which ending path is pursued.