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If you read the book HALO: The Fall of Reach, then you would know that AIs are cloned from parts of human brains. Cortana was cloned from Dr. Halsey. Being that SPARTAN John 117 was Dr. Halsey's favorite Spartan, Cortana chose him. That's why Master Chief has Cortana with him so much, and why they have a special bond, almost like love.

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