Question: When John said "I order you not to go", why didn't that work? Doesn't the T-800 have to do what John says?
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Answer: The T-800 has been learning since he has been with John and Sarah. John specifically has been teaching him to have compassion for human life. Stopping Skynet from ever coming to be is the ultimate way to protect humanity, even more important than following John's order to stay with him. In short, he has overcome his programming and is making a selfless sacrifice.
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