MottledMango147 on the waypoint brought two theories that seem rather plausible:

Theory 1: As the HuntTheTruth Episode 1 podcast said, Master Chief (John)'s flashclone lived to age 12 at least, and ONI declared him dead at age 6. What if John's flash clone didn't die early? This podcast hints at it. What if John's clone grew up and lived a normal life, while the original John (The Master Chief) became a spartan. What if... John's clone... is Agent Locke? Crazy, I know right? But here is why. Locke seems to want to "Replace" the Chief, he seems angry at the chief in the live action trailer. This could be because he is jealous. Jelous that John got to become a hero, while he was nothing more than a mere clone al his life. It could explain all the promotional art showing Chief and Locke face to face, or Chief below locke as a reflection (when Halo 5: G was first announced there was an art work that showed Locke and Master Chief standing upside down from each other, like they were a reflection). They are one in the same. Agent Locke is John's clone. However this theory has one major flaw. John is white and has brown hair, while Locke has brown skin and black hair. They can't be clones if they look so different. It could be possible that Locke got plastic surgery to make himself look different from John, because he wants to be an individual and not a clone, a mere shadow of the Master Chief.

Theory 2: The Master Chief wasn't the original John that got abducted, the orignal John lived his life normally. The Flash Clone never replaced John. John was cloned and returned to his parents, the flash clone was the John that became the Master Chief. Cortana asks Chief in Halo 4 "wich one of us is the Machine?" Chief is has been a clone based off the real john this whole time, and learning this has damaged his self esteem even more. Perhaps thats why he does an unknown act wich deems him a "traitor".