Theory Chief gets kidnapped at 5 and his clone is then sent out Chief goes through spartan training and as a result his imprinting doesn't root like it's supposed. His clone however doesn't and instead they take root and he lives through his programmed death. Clones becomes very much like the ISO didact and his violence and enhanced strength start showing He goes through the normal imprint changes as such he gets bigger and stronger than a kid his age should. Insurrectionists show up, they see this kid is strong and smart as hell. They recruit him. Due to the ISO didact imprinting he develops almost parallel to spartan chief. Now years later chief goes missing and he steps in to replace him. The people that were talking to Halsey in the beginning of halo 4 were really trying to replace him, but needed to know if stripping his personality was necessary for his great abilities. As such they never did, they just gave him spartan training and stuff, chief comes back but leaves again to find cortana. Clone chief, let's out the ISO didact in him and betrays humanity. Locke is charged with going after him but goes after the wrong chief.