I'm think that the whole thing was a lie, since the reporter guy said that most of his contacts were given to him through ONI. I'm guessing that ONI is trying to keep the Spartan-II program a secret because they don't want it getting out that the spartans were kidnapped and pretty much tortured into war machines. By torture, I mean that they had to go through augmentation. Or maybe John would just escape Dr. Halsey on practice days, and when he stopped showing up was when the physical augmentation began?