Puppet Master: We have been subordinate to our limitations until now. The time has come to cast aside these bonds and to elevate our consciousness to a higher plane. It is time to become a part of all things.
Major Motoko Kusanagi: If a technological feat is possible, man will do it. Almost as if it's wired into the core of our being.
Section 6 Department Chief Nakamura: Nonsense! There's no proof at all that you are a living, thinking life form.
Puppet Master: And can you offer me proof of your existence? How can you, when neither modern science nor philosophy can explain what life is?
Major Motoko Kusanagi: You talk about redefining my identity. I want a guarantee that I can still be myself.
Puppet Master: There isn't one. Why would you wish to? All things change in a dynamic environment. Your effort to remain what you are is what limits you.
Major Motoko Kusanagi: Just a whisper. I hear it in my ghost.
Major Motoko Kusanagi: I mean, have you ever actually seen your brain?
Section 9 Department Chief Aramaki: What is it? Artificial intelligence?
Puppet Master: Incorrect. I am not AI. My codename is project two-five-zero-one. I am a living, thinking entity that was created in the sea of information.
Batou: There's nothing sadder than a puppet without a ghost, especially the kind with red blood running through them.
Major Motoko Kusanagi: If we all reacted the same way, we'd be predictable, and there's always more than one way to view a situation. What's true for the group is also true for the individual. It's simple: Overspecialize, and you breed in weakness. It's slow death.
Chosen answer: The Ghost is your spirit. In the end yes, they both merge,making a new entity, not just a human/cyborg and an AI, but a complete new entity - the whole is more than the sum of the parts.