Excerpt from the Chaos Pool:
The Doctor and the false Amy have lost sight of the dog creature that was leading them through the darkness, but there’s an archway ahead of them so they move through. They enter a cave system and are glad to be out of the rain, but there’s no sign of the animal. The Doctor reveals to his companion that he knows she’s an impostor and he holds up a mirror that shows her appearance has started to change back into that of Zara. He says he realized the truth some time ago, but he didn’t say anything in the hope that she might lead him to the real Amy. Zara reveals that Amy is inside the satchel and the Doctor is furious because he knows that could kill her.
So who is the imposter Jack or Claire? The music box was a gift from Christian to Claire. We know however that Jack has been drawn to his reflections for a long time now. The airplane bathroom: Jack finds himself staring at his reflection in that mirror. His scene where he is trying to remember where he got his appendix scar. He was staring into the mirror. While in the temple he is caught just staring into the water that is the moat around the temple. The reflection that we see is blurry and reminiscent of the Marshall staring at his reflection in the Key to Time: the Armageddon Factor episode. The lighthouse episode where he is surrounded by mirrors and he ends up breaking them.
If I were to guess about what this all means could it be that Jacob found a loophole in the form of Jack. Is the appearance that is hiding itself in the mirror in fact Jacob who took over Jacks persona? Is Jack dead somewhere on the island and we just don’t know it. The same could also be said about Claire when it comes to her being dead. We just saw Aaron abandoned and her missing. I believe one of these two or perhaps both could contain the consciousness of Jacob (His counter to the loophole).
When it comes to who is good and who is bad I would have to say neither and both. I believe that they need each other to balance things out and one without the other would lead to chaos for everything.
The Chaos Pool: