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I have been cooking up a convoluted theory in the back of my mind to explain circumstances where WHH is NOT accurate. Most WHH theories use some examples to claim that The Incident was caused by the 815ers, and that everything that we saw unfold is unchanged from how it had unfolded in the past. For example, some WHH theories point to the fact that it appears that Daniel has been shot by his mother in the past, so that implies that we're seeing events unfold as they have already unfolded.
I think that WHH is true to a point, but that a significant event can change enough things at once such that course correction is impossible. A nuke going off is one such event. The failsafe being turned off was another.
I also think that "the rules" that Jacob, MIB, Charles, and Ben are playing by involves not altering certain things in the timeline that have already played out. I believe that all of them are aware of how some future events resolve and that they are unable to alter them without course correction taking over. This is why none of them are able to kill each other - they know they are all supposed to be alive in the future.
For this theory, assume that Jacob is capable of time travel, and immortal from the perspective of being ageless. Also assume that
My theory is that there have been a SERIES of time loops on the island that have been affecting island history, and that we have been seeing the latest attempt to change history. All of the visitations and events on the islands have been in different loops that are basically layering on top of each other. Some of these loops could be consolidated, but I think this theory goes a long way to explain both the rules, and exactly what MIB was saying to Jacob. I also think that there's a little more to explain about Desmond, but I'm not sure how he fits in. Rather than explaining my reasoning, I will just lay them out:
Jacob and MIB are on the island and are aware of how to manipulate time to some degree. Something catastrophic happens in 2008 that is a result of human action. MIB advocates letting it run its course while Jacob advocates changing the past in order to avoid the catastrophe. Jacob goes back in time...
Jacob arranges for the Egyptians to visit the island, who built the Temple and the other ruins. They become the first Others. They attempt to use their technology to change the course of time, but the catastrophe happens anyway, partly due to the fact that they end up fighting amongst themselves. Jacob goes back in time again...
Jacob arranges for the Black Rock to visit the island to provide an injection of European thinking and technology. The first instance of this is when we saw the Jacob/MIB discussion at the start of "The Incident". They fight with the Others, and then eventually assimilate. This is the first loop that Charles and Eloise are brought to the island. History runs its course, and the catastrophe happens again. Jacob goes back in time again...
Jacob has the Others set up DHARMA in order to bring scientists to the island in the hopes of being able to undo the catastrophe. They fail, partly due to infighting between Charles and Ben. Jacob decides that the basic problem is that human science is not advanced enough to understand the catastrophe in time to prevent it. Jacob goes back in time again...
Jacob instructs Eloise to raise Daniel to become an expert in modern physics. This is so that he can send him back in time to the 70's which his knowledge from 2004 so that he has four more decades to fully study the catastrophe in the hopes that he can come up with a way of dealing with it. The freighter is sent for the first time in this loop to deliver Daniel. Daniel decides that the best way to alleviate the Incident is to detonate a nuke at the Swan. There isn't enough time to put this plan into action before the catastrophe because obtaining the nuke is so difficult by that point. Jacob goes back in time again...
Now that Jacob has an actual plan of action, he sets up the US ARMY to bring a nuke to the Island for testing in 1954. The Others gain possession of the bomb. Daniel is sent back again but is unfortunately shot by Eloise before he is able to put his plan into action. Jacob goes back in time again...
LOOP 6 - the loop the show starts in
Jacob arranges for 815 to crash on the Island. Desmond is also needed to trigger the crash (when they became aware of his flashes, Eloise and Charles both had to guide him to stay on the correct path). The intent is to deliver a core group who will, at the right time, believe Daniel, and help him carry out his mission. Eloise knows she's going to shoot Daniel again, but goes through with the plan anyway. This attempt succeeds in that the nuke is detonated on schedule. Whether it works to avert the catastrophe or not will be revealed in season 6, but it will mean something new for the time stream.