Towering skyscrapers loom over the people of Japan with massive advertising screens waving and beckoning at passersby, a hum of an activity both downtown and farther provinces. And yet, in spite of the buzz that practically electrocutes daily life, technological advancements have begun to blur the lines of both man and machine. Cybernetic enhancements, prosthetics and false bodies have successfully become commonplace in society, challenging the definition of humanity and individuality in the process.

Motoko Kusanagi—one of the many victims of this era—suffering from an identity crisis that put her mind at odds with her own existence. Though she does not have to worry about death in a technical sense due to her ability to transfer from body to body, she was always concerned with her present condition. It didn't help that the company you both worked for created your synthetic bodies with possible artificial memories and as much as you tried to ease her worries, you felt your own anxieties slowly bubbling up to the surface.

Whether you liked it or not, you both were cyborgs, built and manifested with the intent of the manufacturer's expectations; and one of those expectations happened to be the containment and investigation of an awakened artificial intelligence known as, "The Puppet Master" that had gone rogue from the Foreign Ministry's hidden agenda. You always had your skepticism of your superiors but not once did you foresee the creation of a program to do their dirty work— you, Motoko and Batou unknowingly assailants.

After Motoko chases after the Puppet Master, you hear that she had been assassinated only to be proven false by Batou. Hearing this, you quickly follow him to the hideout to reunite with her— or what was left of her.

When you see her, she is but a smaller version of herself; a childlike form, if you will. She claims that she is neither Motoko nor the Puppet Master, rather a new entity entirely; one that will embark on a neverending journey to travel the net.

"Will you come with us?", she asks.