Smoke Monster=Security System by Bsti Natosi

If I could provide more precise context to Across The Sea, it would be this theory.

First of all, some people speculate that Mother was a Smoke Being.

There is no real evidence of this, other than that she wiped out an entire village by herself.
I don't think an answer will ever be provided for this, but she did have a physical body that was laid to rest in the cave.
I do believe however, that there was a Smoke Being on the Island, whether it was her or she was able to summon it.
So let's assume what some other people theorize; that the Smoke Being is a culmination of all the darkness in the souls that have perished on the Island.

I believe there must always be two sides on the Island, one Light and One Dark, in order to balance things out. This differs from Good and Evil, but with the same effect-one must exist for the other to exist.

I'm going to assume that the Protector of the Island is endowed with immortality as well as precognition, as my theory stems from that.
So here's my twist:
Mother had always wanted Brother to take over the mantle of Island Guardian. But with Jacob, she wanted as Island Protector.

In other words, she wanted him to become the Smoke Being, the judge of men, the security system that Danielle and Juiet referred to.
The role of Protector is to keep man from ever discovering and exploiting the Light.
The role of Guardian is to keep the Protector from ever leaving the Island.
Mother discovers that Brother has the strong, singular will of leaving the Island, thus abandoning his role as Guardian.
With precognition, she determines that events must, and will, play out a certain way.
First, she knocks Brother unconscious. Then she summons the Smoke Being to kill the villagers while she drags Brother from the well. Then the Smoke Being destroys the well.
She leaves Brother's game at the camp so he will know it was her doing. She anticipates his anger and need for revenge because she as destroyed his only means of escape.
She then moves to Plan B: make Jacob the Guardian instead of Protector.
She sends Jacob off for firewood and returns to the cave, where she knows Brother will arrive.
And just so, he stabs her before she can speak, and asks her why she won't let him leave.
"Because I love you" she says.
With the precognition, she anticipates that Jacob will also have a need for revenge and send him to the Light, where he can never escape the Island.
Thus, the roles she had intended are reversed, as she knew that the Guardian could leave the Island but would never forsake it.
If Brother had become the Guardian, he would leave the Island and never return, leaving the Protector unchecked and the balance needed nonexistent.

The role of Guardian is to protect the Light from mankind.
The role of Protector is the security system that has the ability to utterly destroy all foreign elements without being destroyed itself.

There are some holes in this, I know. But I kind of like it as a twist in the story.