But we don't know protecting the Island is what Jack is supposed to do. He is there to do something important yes, but it could be anything.
The realities are going to merge, or the alt reality is going to affect the Island reality in some way or vice versa. Even if Claire is made the new MIB and the rest get off - where does that leave the alt reality? I think either it's there to bring someone back to the Island, or its there to take them off and back to the lives they were supposed to of had. If its the latter case, Claire will be and have Aarron anyway.
I still can't shake the feeling that this is 'the end', as in whatever happens, I don't think the Island will need protecting anymore or even have a conflict of dark vs light. It only ends once, and the time for that is the finale.
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