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Now before I delve into this too deeply, I would just like to say that I realize this idea may be over-analyzing the situation. That being said, here is an idea that I'm not sure has been talked about yet.
When Locke makes his way back to Civilization after turning the wheel, we see his story in trying to recruit the oceanic six. We all know how it ends. Ben kills Locke and covers it up by cleaning up the crime scene.
Now, I really thought about this and it was strange to me that he would do that. I mean, here's a guy who we all thought to be pretty evasive when he wants to be and for almost his entire life he's been on the Island, albeit he's ventured to and from the mainland. My question is why go through all the trouble of cleaning and wiping up finger prints if he wasn't afraid of being found out? I realize he had to make it seem like a suicide, but we all saw the extensive work he put into the room to clean away any idea that he was there. What does he have to hide? oh and where did he pick up the sweet post-murder skillz?! XD