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From Ab Aeterno we know that the Statue of Taweret and presumably the other ancient ruins (including the Temple) predate the arrival of the Black Rock and the first modern Other, Richard Alpert. Given the depiction of the Smoke Monster in the chamber below the Temple, it is fair to assume that the Black Smoke existed since this time. Far from the Temple being a place of refuge from the Smoke Monster, this chamber appears to have acted as its dwelling place, with its function being that of a security system (possibly even protecting the Temple from the Man in Black, though he would not have been a significant threat prior to the merging under my theory).
Its composition would likely consist of exotic matter similar to that found near the Orchid Station, charged by the Island’s unique electromagnetic energy, both of which the Island's earliest inhabitants were capable of crudely manipulating.
According to his own account, the Man in Black was once an ordinary human being. His crazy mother shaped his negative attitude towards mankind, believing that it was perpetually doomed to corruption. I suspect he and his mother both belonged to the Island’s original population (whom Jacob would have brought for an as of yet unrevealed purpose). The Man in Black’s growing malevolence would not have been an issue if he remained simply human, as he could have been exiled or eventually would have died of old age, but he somehow became merged with the Black Smoke, resulting in the modern incarnation of the Smoke Monster and the subsequent annihilation of the Islands native population.
Since that time he has been subject to both of his natures. This is evident in the fact that Ben was still able to summon the Black Smoke to ward off the mercenaries, and in the real Locke’s personality at times emerging in Fake Locke’s actions, such as his retort to the mysterious boy, “Don’t tell me what I can’t do!”
Meanwhile, Jacob (whose own nature is neither merely human nor angelic/divine) had served as his jailer, hoping to correct his views on human nature at the same time. However, even with his jailer now dead, the jail remains, as it is the Island’s unique nature that was both the source of his abilities and the means of his imprisonment. It is for that reason he must work quickly to devise a means of escape, before a Candidate steps in and takes up Jacob’s mantle.
However, Jacob’s successor will not merely be another jailor. Rather, that individual (my guess is Jack) will devise a means by which to separate the Black Smoke and the Man in Black. The result will be that the Black Smoke resumes it proper functioning and in doing so judges the Man in Black for his crimes, resulting in his execution.
As comprehensive as my theory is, I have not yet found a rationale for the Rules. If anyone could contribute an explanation it would be welcome.