Two theories, enjoy
Project YoRHa is an extension of Project Gestalt. The original goal of Project Gestalt is to preserve human souls through difficult times, but it failed and ended up annihilating souls. Project YoRHa is a backup plan whose purpose is to help androids and machines become human by teaching them various emotions/giving them souls.
Project YoRHa was created by the machine hivemind. The hivemind views human emotions as something that will lead to demise (all machines who end up having emotions killed themselves or went crazy. Ex. Adam, Pascal, Pascal's children, Father Servo, Engles, the flying racer robot, amusement park boss etc.). The hivemind used machine cores to create YoRHa; the war between YoRHa and machines is to give androids and machines purposes and keep them occupied. (Machines who had nothing to do tend to get bored, cut themselves from the network, and start to have emotions. Ex. Pascal's village) It also tries to eliminate individuals who already have developed emotions (send an army after Pascal&children, "hack" YoRHa soldiers to hunt down 2B&9S). Project YoRHa is the hivemind's attempt to keep the world free of emotions, thus saving the machine species.
Let me know what you guys think about project YoRHa!