I have had a week to contemplate season 5’s finale. I’ve talked with friends, I’ve read the blogs and theories, and let my mind wander for days. Although my impression of this year’s finale was not that high, I am at least pleased with what is to come next year from the Jacob vs. Samuel dilemma that was introduced (I use the name “Samuel”, because that is what he is called in the casting notes from producers, even though it may be changed since Jacob was originally listed as Jason). Theorists have contemplated that this character is Jacob’s Father, Brother (Esau?), Anubis, Ra, Moses, and even Satan. Although those all have interesting supporting concepts, here is my theory.
Jacob and Samuel represent god-like representations or servants of good and evil. Jacob, always wearing white, is the protector of the island. When Ilana asks Richard “What lies in the shadow of the statue?”, he replies in Latin with “Ille qui nos omnes servabit.” This translates as “He who will protect/save us all.” Although he does look scared when he utters the phrase, the show is trying to tell us that Jacob is the protector. He saves Sayyid from the car crash, he saves Locke after falling out the window, he saves Kate from being punished for stealing. I believe, that for some reason he wants to help the LOSTies and protect them. Although we do not know why yet, there is going to be significance to why he physically touches everyone in the finale episode. Perhaps that act provides some sort of god-like protection in the future (which is why they survive the plane crash, smoke monster, and other island dangers).
In contrast, Samuel always wears black and represents evil. Although we don’t know what happens to Samuel since the 1800’s flashback, somehow he “dies” from his natural body. Therefore, over the past 5 years of LOST, Samuel has taken form of other bodies on the island that we could not yet explain. But now, knowing he was in the form of Locke for most of this season, we know what he is capable of. Samuel has been the dead visions of Christian, Alex, Locke, Eko’s brother, Horace, Ana Lucia, and Libby. Samuel can only take vision of one person at once, which is why Locke disappears when Samuel becomes Alex to Ben in The Temple. Somehow Samuel is unable to physically touch people while in human form, which is why his “loophole” to kill Jacob, is to convince Ben to act on his behalf. This is also seen in how Christian is unable to help the real Locke up after falling into the well and breaking his leg. By the way, Locke wears a dark suit or shirt the entire time he is embodied by Samuel, Eko’s brother is in a black priest outfit, Christian is seen in a black suit, and Alex wears black when presented at The Temple.
Finally, Samuel is also the Smoke Monster. In The Temple, there is a heiroglyph that depicts the Smoke monster vs. an Egyptian statue. Since Jacob lives in the shadow of the statue, and thus represents that deity (Egyptian god Taweret, not Anubis), Samuel is the Smoke Monster that is drawn standing next to it. The best explanation of this I have seen is that Jacob and Samuel represent SOBEK and APEP from Egyptian mythology. A good explanation of this can be found in the blue link above. I believe the truth will be something of that nature.
Season 6 will spend the majority of the time focusing on the history of these two characters and how they manipulate the people around them. In truth, “the island” could be completely normal, and all the mysterious acts are caused by their direct actions or involvement. Did the Island make Locke’s legs work, or did Jacob? The whole series could be explained by how Jacob and Samuel manipulate man’s actions with their divine powers. The tapestry Jacob weaves is a timeline of events that have happened and will happen on the Island. Jacob represents the “eye” at the top, and the people he has touched represent the people below him, and below them are things that happen on the island.