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I simply had to lay them out.
Origin of the Island
- Where did it come from?
- Why was it built?
- What is it? Is it a geographic feature, or an artifact?
- Who were the first inhabitants of the island?
- What is the "source?" Is it something natural on the island or was it put there by someone/something?
- What is the relationship between it and the smoke monster?
- What is the connection between the source, the whispers, the time traveling, the dead on the island, the healing properties?
- Why were there so many Egyptian references in the show? These include countless hieroglyphs, the lighthouse and counter on the swan station. Why did the others speak Latin?
- Who built the temple? Was it there before Jacob and his brother arrived on the island? Was it there before their mother arrived on the island?
- Who were Dogen and the others who lived there? What was their relationship to the other "others?" To Ben, Widmore, Jacob, and the smoke monster?
- What is their origin? Who was their biological mother? Why was she killed?
- Why did Jacob's brother want to leave the island so much? Later, why did he tell Kate that he wanted to go "home?" Where did he consider his home, if not the island?
- Was he dead when he went into the cave of light?
- What was his connection to the black smoke?
- Why couldn't he be killed?
- What was the significance of "speaking to him?"
- What were the nature of Jacob's powers?
- Was his job to keep the smoke monster on the island, or to keep people away from the island, or both, or something else entirely?
- Why did he wait so long to tell the candidates about why they were there?
- How was he able to continue to communicate after he was dead?
- Why did his body "disappear" when he was stabbed by Ben?
- Once he died, why couldn't the smoke monster leave?
- Why couldn't Jacob or his brother "kill" each other? How did their adoptive mother make sure they couldn't?
- When did those events occur? Why did the bodies appear to have been there only a few decades, while the deaths seemed to occur in the distant past?
- What were the cave and lighthouse?
- Why couldn't the smoke monster travel across water?
- What effect did Jacob's death have? Why wasn't he freed when he died?
- Who were the "they" that Jacob referred to as coming after Ben stabbed him?
- Did he want to die? Why was he trying to antagonize Ben before he was stabbed?
- What was the role of his "faction?"
- What were the whispers? We were told that they were caused by Michael and the others "who couldn't move on," but what does that mean? Why were they only heard on the island?
- Why were they heard when the smoke monster was nearby?
- What was the smoke monster? Did it exist before Jacob's brother went into the well? Was it supernatural or was it a kind of technology?
- What was the nature of the noises it made? Why did Rose think that it sounded familiar in The Pilot? What were the "mechanical" sounds?
- Why didn't Richard die when it grabbed him in Othersville?
- Why did it kill some people and not others?
- What was the cabin? Who built it? Why was it built?
- What was the "sickness" to which Danielle and those at the temple referred? Did Claire succumb to it? Did Sayid succumb to it?
- Was it related to the pregnancy problems?
- Was it real or just a fabrication to control people?
- Why were the numbers everywhere?
- Did they have any significance beyond the numbers that Jacob assigned to the candidates?
- Why was Walt seen in the jungle by Shannon? And by Locke when he had been shot by Ben? Was that just the black smoke?
- What was behind all the strange occurrences that surround him in the first season?
- What did the others do with Walt when they abducted him in the second season?
- Why couldn't Michael commit suicide?
- Why did he have to come back to the island on the freighter before he could die?
- What was the Dharma initiative?
- Why were they on the island?
- How did they find the island?
- Were they involved in bringing Jughead?
- Did they know about the island's "properties" before they came, or did they discover them by chance while doing other things?
- Who were the Degroots?
- Who was Alvar Hanso?
- How was the Valenzetti equation related to Dharma? the polar bears?
- Was the Swan built to actually control the power?
- What happened when Desmond activated the fail safe? What would have happened if he hadn't activated it?
- What was the true purpose of the Pearl?
- What was the DI's status as of 815 crash? Why did the pallet drop happen?
- What was Kelvin's relationship? How did he become involved?
- Why did Pierre Chang use false names in the movies?
- Who was he? Where did he come from?
- What was his final plan? How did it involve Desmond?
- Why couldn't he and Ben kill each other?
- Who were all the people that Ben had Sayid kill?
- How was he able to return to the island on the submarine?
- Why did he send Faraday on the freighter?
- What was his purpose in sending the freighter at all?
- What was the nature of the missile experiment?
- What was the church "mechanism" that allowed Eloise to find the island and send back the returnees?
- Was the detonation of Jughead "the incident?"
- How were the Lostaways :-) able to survive the detonation? Were the others present able to survive?
- Had the detonation always occurred, or did Jack change the past when it was detonated? If it had, what happened between then and the crash to Pierre Chang?
- What was the effect of the detonation? Did it sink the island? Was it entirely unrelated to the FST?
- How and why did he become unstuck in time?
- Why was he "the key?"
- Why was he the only one who could do whatever Widmore wanted him to do?
- Why couldn't he put the "cork" back at the end of the finale? Why did Jack insist on doing it?
- What was his connection to the FST?
- What was his connection to Eloise and Widmore?
- When did the FST come about?
- How did it come about?
- Was it entirely "Jack" related?
- What was it that the characters needed to remember? Why did they need it to be reminded and of what?
- What happened when the cork was removed at the source?
- What happened when Jack put it back?
- What effect did it have on Locke/the smoke monster?
- What effect did it have on anyone else?
- Why couldn't Locke kill Sawyer when he was no longer a candidate?
Please correct me if any have been answered and please add any that I missed.