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After viewing "Across the Sea," we are still left with ambiguity regarding the role of good versus evil in relation to the struggle between Jacob and his brother, The Man in Black. There are no innocents in the this narrative... aside from Claudia, the true mother of the two boys.
"Mother" killed Claudia. Jacob's brother killed "mother." In turn, Jacob killed his brother.
"Mother's" reason for killing Claudia was, in her words, in order to keep the two boys from becoming evil. She acted as judge, jury and executioner to kill a woman who, from all appearances, had done nothing deserving death.
When Jacob's brother killed "mother," his act could be justified. "Mother" had not only killed his true mother, Claudia, but had also killed numerous people with whom he had been living for many years. This was an apparent act of pure evil. "Mother" was a murderer. The traditional penalty for murder is the death penalty which is still recognized by much of the world as the proper and just punishment for this crime.
When Jacob through his brother into the "cave of light," he knew full well that it would kill his brother, even if he was unaware of any potential unforeseen circumstances. This was an act of vengeance. Jacob executed his brother, choosing to ignore his "mother's" actions in killing the other people on the Island and his own biological mother, Claudia. Jacob appears to be a man in denial of the truth.
The conclusion here is that Jacob's brother, while certainly a flawed individual, appears to be acting on the side of truth and justice. Yet we know that the Man in Black has been presented to us as being the great antagonist of LOST. How do we reconcile this?
I see two possibilities:
1. We should not equate the identity of an antagonist with "evil." MIB may be the shows antagonist because he is working at cross purposes to those who have been presented as the protagonists. When you watch a baseball game where your favorite team is playing against their biggest rival your experience is directly opposed to someone who is pulling for the other team. Neither team is objectively "good" or "evil." They simply both want to win the game. In war, "Good and Evil" often boil down to which flag you are waving. "Our" flag is good while "their" flag is bad. The opposing faction also has an opposing view on this.
2. Possibility number two is the "The Man in Black" is NOT "Jacob's brother." Instead, just as the Smoke Monster has taken the form of John Locke, he can take the form of Jacob's brother. When Jacob sent his brother down the stream into "The Cave of Light," the cave dimmed and the Smoke Monster appeared. It is quite possible that something quite other than Jacob's brother is what emerged from the cave. Perhaps some kind of life was awakened.
Please post any other possibilities or problems with these theories.