In the near future, human organs are enhanced by the cybernetics technology developed by the powerful Hanka Robotics Corporation owned by Cutter. Dr. Ouelet is responsible for the development of the secret project 2571 of a full mechanical body to be connected to a human brain. She uses the brain of a young woman that lost her parents in a cyber attack as subject of a prototype. One year later, the woman is ranked Major and has joined Section 9, an anti-terrorist division commanded by Chief Daisuke Aramaki, working with agents Batou and Togusa. She needs to use a medicine to help the integration of her brain with the mechanical body and has no recollections of her previous life. When Section 9 hunts down the terrorist Kuze, Major learns the secrets about Hanka Robotics and the experiment she was subjected. Now she faces her ultimate enemy: Kuze, a criminal who has managed to hack into the brains of androids and control them.