Last Night, the episode heavy on mythology aired but it left viewers in a split half loving and half hating it. Personally I felt that the episode answered more questions than people realized. As a package it was missing the right delivery. The Delivery was cheesy, seemed something out of a poorly woven together fantasy novel, but only at first glance. After reading other peoples theories and recaps and adding my own opinion, the light is starting to appear through the clouds, or in this case a river in the middle of a jungle.
Remember the Sickness? Or Being claimed? MIB when talking to Kate on the beach compared Claire to his Mother who we have seen for a whole episode. Claire's sickness was similarly compared to Sayid's and Rousseau's comrades and other occasion where the sickness occurred. As Dogen said, It is "Darkness". In this episode we see a direct allusion to the light, in which "Mother" claimed every man has a little part of in. Although this light is said to be life death and rebirth, I think the heart of this light is an energy, or even cheesier, a love that fuels the person. As we can see, when Sayid is claimed he begins to feel nothing, The Light has been taken out of him, because the Darkness has filled him, or more specifically MIB has taken him. Although mother did show signs of affection especially towards her sons, she also had that crazy factor that was present in Claire and Sayid, and perhaps this is why she loved MIB more than Jacob.
Now before you say, oh well Sayid turned out to be good in the end. After what? Desmond, the variable, the person who like MIB has also felt the light as a result of turning the fail safe key. If you remember when he turned the key and was consumed by the bright light in the hatch, he also similarly appeared in the middle of nowhere just like MIB did down the river. However, with one key difference, Desmond was not consumed by hatred and anger when he was down there, he was a good guy. Unlike MIB who because of his lost village and being trapped had become angry at the time of being exposed. If MIB was good like Jacob and went down that well would he still be the Pillar of Smoke? Possibly not, but unless the writers address it we will never know.
MIB as a result of being consumed by the light has stripped all the light within him, he is no more a person of emotion or cmpassion. He is as Jacob says he is, malevolence, evil, and the darkness of man. What will happen if MIB goes out into the real world? All the people will turn into like sayid's. There will be no more love, it will be greed, selfishness and darkness. Makes sense that he has to be contained now doesn't he? As a result of all the light being stripped out of him he became both the symbol of darkness, and actual darkness in the appearance of physical black smoke.
I would also similarly say that Mother seemed to have the same sickness that MIB and that Claire have and Sayid had. It seems to affect people differently. But basically the Craziness of MIB's mother is very similar to the other people who have also been claimed. Imagine if everyone out there in the world was like this, the light in everyone wuld go out, just as "Mother" told Jacob and MIB.