I don't think Michael was brainwashed at all. You have to remember that a father will do pretty much almost anything to save his son. Michael is not a bad person at heart, but he did make a decision to do something wrong in order to get his son out of this place. I mean it is the same idea as if you could only pull one person out of a deadly car accident and it was your son or a stranger, who would you pull out? Extreme measures cause parents especially to do whatever it takes to protect their children. Yes Michael didn't want 2 kill Libbie, but he went in there knowing he was going to sacrifice Ana Lucia in order to do whats best for Walt. As far as the where are Michael and Walt...that little boat could have sent them to the place where the sub is, which carried them off that island. I don't think they are coming back.

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Because all we really need to survive is one person who truly loves us. And you have her.