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Johnson was a Spartan 1. The first class of Spartans were just marines given genetic enhancing drugs at and adult age. If I had to guess he was probably put on a high stakes mission only certain people could withstand at the time. Or the drugs messed with him enough to developed borene's syndrome in the first place instead of dying outright from the radiation.
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It wasn't keeping the Spartan 1 project a secret it was keeping Johnson's condition a secret. If ONI found out about how Johnson survived the flood they would kill him so they could study his body. Chief didn't want Johnson to die.
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Ah, now it makes sense. But I'm still confused on how when chief saw that video log of the flood and Johnson's team, how did he survive that? Sure he's immune to the flood but how would he have escaped?
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Edited by Stoneenergey: 3/11/2015 5:18:20 PMIn the book "First Strike," they do a really vague explanation. Since the flood spared him he kinda just escaped. That's literally their explanation. You might have to check the halo wiki for a better explanation
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So why is it that Chief and him had to keep the Spartan-1 program a secret?