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If you saw the special ending, yes, he was blown up along with the halo ring
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He was cloned, Gliches in the cloning process resulting in a change of skin pigment.
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Seargent Johnson was immune to the flood because of his prolonged exposure to plasma grenades during a battle. But in the book he and his marines escaped on pelican
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Interesting thing is, If I remember correctly, the Boren's syndrome was actually from (or a cover for, I don't remember which) his Spartan I augmentations
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Your right.