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1. It is suggested that the Spartan 1.1s didn't inherit their augmentations, but were given them after birth through chemical injections.
It was suggested by a crooked and "stupid" Cop. I don't know if I would consider him a reliable source. All he managed to do is figure out she was augmented but how would he have known someone had actually injected her with anything?
From what I have been able to gather from reading through the Axon Clips, she had a pretty normal childhood until ONI came to see her at school and tagged her as gifted.
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2. Johnson joined the Marine at 19.
Simple mistake. Easily correctable.
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What if Agent Locke inherited Johnsons Flood Resistance ?!?!?!?!??
I've been toying with this idea in my head, but omitted it from the article. The Master Chief and Halsey decided that giving ONI that information wasn't worth sacrificing Johnson's life. The clues to his supposed immunity were truly lost when he actually died in Halo 3 but if Chief were to learn about a son, then he could consider the possibility that maybe it's not too late to find it?
Of course if Chief didn't want to sacrifice Johnson then he probably wouldn't want to sacrifice his son. Unless they had discovered some new information which could help? Maybe find some of the Librarian's research and combine them to find the Cure she had sought for so very long? ONI is aware of the ancient human cure and that the Librarian and Primordial tried very hard to find it and failed. He could be the missing piece of the puzzle.