THE SECOND BIG MISTAKE
Long after the Egyptians were gone, pregnant Claudia washes up on shore and “Mother” is there to help her deliver her baby and we later learn that the “baby” turns into “babies” as twin boys are born. At that point, Mother is in the role of Father Time i.e., she is the protector of the island and time but she is tired and she wants out, so she murders Claudia and manipulates the two boys into taking over her role. The two boys make a perfect duo; one boy is innocent and faithful enough to do what is right for the island, and the other is willing to lie and kill to get things done (a perfect balance). But something bad happens here that I don’t think even Mother could foresee. Jacob throws his brother into the light/time cave and at that point the smoke monster (the past as an entity) becomes a person via the merging of it with the MIB. The smoke monster had existed prior to this incident (as we see in the Egyptian art), however I don’t think it had ever been merged with a human soul before, this gave the smoke monster purpose. The smoke monster was no longer a mindless cloud of past memories, it was now a very mad person whose body was removed and whose soul was merged with a pillar of smoke and hurtful memories.
When the MIB is in the primitive well speaking with his mother, he tells her that they are going to attach the wheel to a hole which will make a system that channels the water and the light and when he turns the wheel he will finally be able to leave the island. Mother knows that the MIB is correct and she responds rhetorically “how do you know all this”? It isn’t long after that when Mother slams the MIB’s head into the rocks knocking him out. She proceeds to kill all “his” people and fills in the well which makes the MIB extremely perturbed and in turn he kills Mother. Mother then thanks him and dies. The important part of that story is that Mother knows the MIB is right. She knows that by manipulating time, the MIB will be transported off the island and likely will never return. Mother doesn’t want to lose her replacement protector because she wants a permanent vacation. So she takes it upon herself to destroy the early version of the time traveling machine. Therefore, even though Mother got her replacement, I don’t think she envisioned Jacob throwing his brother down the cave and creating a monster even bigger than before. The sin, pain, and hurt of the past was growing, but now it had purpose.
At some point somebody eventually uncovers the well and installs the wheel correctly, but their identification is not known and frankly somewhat irrelevant, all we know is that happens between the time of the MIB’s death and the Dharma Initiative.