The Hanso Foundation is actually responsible for the existence of the Others (indirectly), the Monster (directly), Jacob (directly) and many aspects of the Island.

As I see it, the Dharma Initiative was making good progress on accomplishing the task given to it in attempting to restructure elements of nature to adjust the equation and therefore the numbers (4,8,15,16,23,42) as the Sri Lanka video discovered.

Unfortunately, something went wrong! The fall out of the cataclysm that followed led to a number of unexplained anomalies of nature, including the Monster and the various healing/destroying attributes of the Island.

As it happens, the true effort of the initiative was not actually being progressed above ground in Othersville as they were merely a life support system disguising the true nature of the project whilst engineering supplies and materials for the actual effort. The real progress, unbeknownst to most of the above ground Dharmas, was being pursued underground in the linked experimental areas of the hatches and the central Laboratory. When this cataclysmic failure occurred, the central Laboratory imploded blocking all the links from the peripheral hatches.

Jacob himself was one of the scientists in the central Laboratory at the point of failure and the effect that it had on him was to push him partially into another dimension. Jacob can therefore only be seen fleetingly in our dimension when ‘positioned’ right. This same disruption of nature caused the creation of the Monster.

From the perspective of the monster, it’s all Jacobs fault. It hates him, it knows exactly where he is at all times and is bent on eliminating him as the cause of its creation and the anomaly of nature that holds it in the state it is in, unable to return to its original form. It cannot however get to him, he has become a hermit in the one safe place that he has found as a result of the fall out, he has discovered that, like with the sonic fence, the monster is incapable of crossing the powder which was the waste product of most of the experiments undertaken and has surrounded a small shack with it to hold the Monster at bay.

His only hope of escape is to undo what has been done, in order to achieve this he must discover a mathematician of such genius that he/she could re-engineer the equation thereby leading to the understanding that is required to reverse the attempts that were made to alter it. Therein lies his problem, no amount of searching off the Island has located this level of genius, he therefore has only two hopes of finding it.

One lies in the small chance that an off Islander will arrive at the Island and will demonstrate sufficient special abilities after coming under the influence of the Island to develop the Genius required but this is a very small chance, Walt demonstrated the potential for this and as such has been transported to an experimental hatch which will reveal whether his abilities will ultimately lead to the level of genius required (and hence why Walt appeared to Locke to tell him his work wasn’t complete).

The other lies in the birth of a baby conceived on the Island and matured to adulthood as the very nature of the Island would affect the natural intelligence of the child exponentially. This has led to his obsessive desire to overcome any obstacles preventing the birth of a child conceived on the Island and unfortunately he has a catch 22 to deal with in that the very same disruption of nature that caused him to be dimension shifted and the Monster to be created also causes the abnormal growth of embryo’s conceived on the Island which leads to their and their mother’s death.

For this purpose, Juliet was ‘arranged’ but has so far been unsuccessful. But the thought of half a plane full of people, many capable of conceiving, attempting to leave the Island when they had survived the crash was inconceivable to Jacob. So many potential attempts at finding a solution to the child bearing issue could not be overlooked and Ben was instructed to prevent it at whatever cost to lives or comfort.

Which brings us to Ben, no member of the Dharma initiative could go wholly untouched by the contamination of the experiments being held. Indeed, had they known it, all of them had been affected to varying degrees by the same partial dimension shift as more fully affected Jacob. Unfortunately for them, they were all killed by the hostiles and therefore never discovered that they would have been able to see Jacob in his changed state, that is, all except Ben. As the sole survivor of the Dharma initiative and therefore the only person remaining who had been affected by the contamination, he was able to see him, albeit in a slightly altered state, when he happened upon the shack in the protective circle.

Jacob didn’t reveal his true identity to Ben having knowledge of his involvement in the purging, he did however give him information that led him to have access to the sources of intelligence around the Dharma plants that they (the underground Dharma) originally used to gather information regarding the emerging scientists of the world. This led Ben to achieve almost God like status within the Others thereby securing his place as their leader and also giving him access to the self same resources that the Dharma initiative had used to bring many great, now dead, scientists over the years.

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Please feel free to edit this and fill in ‘shaky’ aspects of the theory. Embellish to your hearts content but please leave the basic thread of the theory intact if you do.