I've come up with a few theories on how the final episode may play out, by reviewing some of the comments characters have said in Season 6.

In the episode "Happily Ever After" Eloise Widmore (e.g. alternative Eloise) warns Desmond that it would be a "violation" to give him information. This implies that there were some rules in place, almost like some sort of peace treaty.

Theory: The Losties will be presented with a choice. Travel back and sink the Island in 1977, killing themselves, Jacob and the MiB, but protecting it forever. However, their alternative lives will all play out slightly differently as a result. Some will like this, others won't. Crucially, they need to be prevented from "remembering" the Island, or at least being aware of the alt-universe, or else they may try to track it down and put the Island at risk again. Thus, Jack (now that he is like Jacob) creates rules to prevent this happening. Jack therefore does his job - protecting the Island forever.

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