Ben is judged for his actions by the Smoke Monster beneath the wall that hid the Other’s Temple. Lots of Island mythology involved here, as this chamber where the Smoke Monster inhabited was filled with hieroglyphics and imagery. Oh, and judgement.
Ben was led to this location by John Locke, who, in opposition to the episode’s title, does not seem dead. Ben and Locke have switched places from earlier seasons where Ben had the answers and John was blindly following with the hope of picking up any tidbit of knowledge he could.
Ben was judged by the Smoke Monster, and then put in his place by the Monster in the form of Alex. Alex pinned Ben against the wall and told him that she knew he was already planning to kill John, but he will not touch him at all. He will follow every word Locke said. Alex’s ferocity revealed that this was not the same little girl who feared her father and anted to get away from him so she could be with Karl.
We have also seen a weakness in Ben. Children. We had a chance to see him abduct Alex from Danielle in a flashback. He was sent originally to kill the woman, but when he discovered the baby, Ben chose to leave her alive.
Later, Ben approached Penny with the intention of killing her to get back at Charles Widmore. He had already shot Desmond and was approaching Penny when little Charlie came out from below deck on Our Mutual Friend, Penny’s boat. The arrival of charlie stopped Ben and made him reconsider the course of action. Desmond, who was shot but far from dead, jumped Ben and beat the bloody hell out of him, dumping him in the water.
Why does Ben pause when there are kids near? Could it have to do with his own childhood, where he grew up without a mother and an abusive father? He does not want to put another child through the same loss? Or maybe it has to do with the fact that subconsciously Ben remembers being shot as a child and could not bring himself to inflict the same kind of pain on another child, knowing that he would have had to eliminate the baby and Charlie as well.
It was possible that baby Alex was just one way to try and make Charles Widmore look bad. I would expect that Ben was already plotting against Charles at this point in history and that he believed calling Charles out as a baby killer in front of the Others would help get rid of the man.
Ben has a new mission. To follow John Locke or to die. But let’s never doubt that Ben Linus has a plan to turn things in his favor. Maybe it will have something to do with the line that Ilana asked Frank:
“What is found in the shadow of the statue?”