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BJ wrote:

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This post will be updated as the seasons progress and questions are answered and new ones are asked.

Please keep this thread spoiler free.

Current Questions (Season 4)
What happened to Faraday and the other people in the zodiac?
What is the story behind Charlotte? Was she born on the island?
How does one move an island?	See Season 4 finale.
Why did Mr Abaddon encourage Locke to go on the walkabout?
When Richard the ageless visited Locke as a child, what was the meaning of the items he showed to Locke? Why did the knife make Richard angry? Was that sand in the bottle the same as the sand surrounding Jacob's cabin?
What happened to Clair when she went off with Christian? Why did they leave Aaron behind?	Claire now seems to have a new personality and is in kahoots with Christian in the cabin.
How did Ben get to the desert in a parka? How did his arm get injured? Where and when did he come from? Ok, so it looks like he arrived there after moving the island.
How did the ship's doctor end up dead on the island before he died on the boat?
Who were the snipers that killed Danielle and Carl?	Turns out they were Widmore's snipers. They also killed Alex.
Who staged the fake plane crash? Ben says Widmore and Widmore says Ben.
We learn that the island won't let Michael die in Manhattan. What's up with that?
Where is Walt now that we see Michael is the mole on the freighter?	Walt is with Michael's mom in Manhattan.
What happens to Jin? Sun makes if off the island and has her baby, but Jin has a grave. Is he really dead or back on the island?	It looks like Jin goes down with Michael on the freighter..
Who does Harper think Juliet resembles, leading to Ben's crush?	The enhanced version of the episode confirms that Julet resembles Annie.
How do the freighters know about the gas and how to find the Tempest station?
How did Harper (Goodwin's wife) appear and disappear so quickly in the woods? What's up with the whispers again?	Note that Harper's diploma has a Hanso Foundation logo.
In The Constant, Dan gives Desmond a formula/frequency message to pass to himself in 1996. Where did Dan get that info?
Why is Miles trying to extort 3.2 million dollars from Ben? Where did that number come from? Who does Miles think Ben is and what can Ben do?
What was the point of the card trick/memory test Dan was doing?	Likely this was to illustrate Dan's memory problems.
How does Kate end up with Aaron?	In season 4, Claire disappears with Christian and leaves Aaron behind. Sawyer takes Aaron and hands him over to Kate before he and Jack head off to find Hurley. We still don't know why Claire left Aaron behind in the first place.
Both Naomi and Ilsa wore bracelets. What do the initials RG stand for?
Who was Ilsa (or Elsa - the german chick that Sayid killed) working for? Who was the golf guy that Sayid killed? Why is Sayid working for Ben killing people?	Sayid started killing for Ben in revenge for Nadia's death.
What's up with the 31 minute time wrinkle discovered by Dan?	In The Constant, we witness Desmond jumping back and forth between 1996 and 2004 in consciousness. We also have the dead freighter doctor showing up on the island long before he is killed on the freighter. Not only that, but he shows up one day before the helicopter which left at the same time he was killed on the boat.
What is up with Jacob's missing cabin?	They found it again with the help of Horace the mathematician's map.
Who is Ben's mole on the freighter?	Michael.
What's up with the bending of light noted by Dan on the island?
Why did Dan (the physicist) cry when he saw the news of flight 815 on tv?
How did a polar bear with a Dharma collar end up in Tunisia?	Hmm, maybe it ended up there after the last time the island moved.
Who are the Oceanic-6?	Sun, Sayid, Jack, Hurley, Kate and Aaron. Jack claimed (in Kate's court case) that 8 survived the crash, so who are the 2 who survived the crash but didn't make it back? Note Jin's grave has a date of death of 9-22-2004.
Who is Matthew Abaddon, the man who visited Hurley in the hospital, and was Locke's orderly pre-crash?	So far we know he put together the helicopter group led by Naomi.
When Hurley came upon Jacob's cabin, we saw Christian sitting in the chair and another person peeking out the window? Who was peeking and how could Christian be there?
Current Questions (Seasons 1-3)
Whose funeral did Jack attend in his flash-forward at the end of season 3?	Locke. grrrr
Where is the island located?	At the time of the rescue the Oceanic rep claimed it was near a group of islands. They traveled 3000 miles to get there after being rescued by Penny's boat.
What is the black smoke?	In season 4, we see Ben summon the smoke monster to attack Widmore's snipers after they killed Alex.
What is the flashy thing the smoke monster did to Juliet when her and Kate were handcuffed?
Why can't the smoke fly over the security fence?
Why do trees explode/vanish?
Where did the food drop come from?	Given Ben's comings and goings to/from the island, it would be pretty easy to arrange a food drop.
How does the island heal people?	We have had hints that the electromagnetic fields of the island may have healing powers. If the island does heal people, why doesn't it heal Ben's tumor?
What causes the pregnant Other women to die? It is only women who conceive on the island that have a problem.
What is the story behind the skeletons (Adam and Eve) with the black/white rocks?
What is the sickness that infected Danielle's group?
What's the deal with the injections? Do they really have any effect since Danielle says her crew was infected? Could they be connected?	Note when Ben and his father first arrived at the island we saw someone being injected in the registration area.
Does the squawking bird actually say Hurley's name?
How did an enormous slave ship get to the middle of an "island?"	In season 4, The Constant, we learn that the Black Rock disappeared but its log was in the hands of a Hanso. It was auctioned off to daddy Widmore.
Why do the props in the hatch change? Is this meant to indicate passage of time?	In season 4, we also see photo frames changing. It is possibly due to subtle changes in the timeline when people like Desmond flash around in time.
What is the significance of Widmore? Pen Widmore was Desmond's girlfriend.	Widmore was videotaped by Ben(?), shown beating one of Ben's men. Ben claims Widmore is looking for the island but Ben has no idea how Widmore knows about the island.Widmore purchased the log of the Black rock in 1996. Widmore Labs made the pregnancy test used by Sun. They also manufactured (or sponsored) Henry Gale's balloon. Widmore Construction had a sign on a building behind Charlie's music video set. This building looks a lot like a set of blocks on Aaron's table when he lived with Kate off-island. Widmore sponsored the boat race that Desmond was in.
What do the hieroglyphics on the countdown clock symbolize?
Is there any significance to the sulfur smell of the shower?
What is the (Pala?) ferry mentioned in the Pearl video?
What happened to Marvin Candle's hand?
Why does the same apparent person use two different names - Marvin Candle and Mark Wickman? He used yet another name in the Orchid video.
Why are the hatches abandoned? What sort of project failure occurred? Is it related to the conflict between the Dharma people and the hostiles?
How did the hatch implode if Locke and Desmond ended up outside in the jungle?
The polar bear's cave contained a dump truck, bones, old rags with a Dharma logo and an old monitor. Where did these items come from?
Why was the orientation film chopped into pieces and why was a piece of the film and an eyeball hidden in the bible at the Swan station?
Who left the burning cigarette in the Pearl shortly before Locke and Eko first arrived?
Why did the helicopter crash? How did the helicopter find it's way to the island if all the beacons and communication systems on the island are kaputt?	Dan gave the pilot specific directions to follow. The helicopter didn't crash, but was knocked around by the passage to the island.
Since Naomi is not working for Penny, who was she working for and how did she get the Des/Penny photo?	She was hired by Matthew Abaddon.
What is the connection between Desmond's monk mentor and the jewellry shop woman? They are shown together in a badly photoshopped image on the monk's desk.
Why was blood taken from Jack and Kate? They also took Michael's blood in season 2. Sawyer's blood could have been taken during his fake surgery where they faked implanting the device in his heart.
Ben seems to have had a relationship with both Juliet and Colleen. What's the story there?	We learn about Ben's jealous ownership of Juliet in season 4.
The Others had nice clean clothes when they were in their own village. Why did they wear rags and why was Mr. Friendly in disguise when they captured Walt, then Michael and the other Losties and why did they have the fake village?
Who is Jacob and what is his list?
What is up with Jacob and his cloak of invisibility?
What is the ring of powder around Jacob's house?
How/why has Juliet's shoulder been dislocated 4 times?
What happened to Annie, Ben's childhood friend? We didn't actually see her body after the gas attack.
Why does Richard never seem to age?
Is Christian really dead? What happened to his body?
Why was Desmond naked when he woke up in the jungle after the blast?
Why can Desmond see the future?	See The Constant, season 4.
In Jack's flashforward, who died? Who was the "him" Kate referred to? What happened to Jack to push him to drugs? Who was the mother/son pair that Jack saved in the car crash?	Kate's "him" is Aaron.
What happened to Kate after her breakfast on the beach with Ben? She seemed to be roughed up before arriving at the cage across from Sawyer.
Was Libby stalking Hurley? Why was Libby in the hospital with Hurley? How was she released from the hospital? Why was Libby in Australia and why was she on the flight?
What was in that wacky paste Locke put on Boone's head?
How did Locke's dad get on the island?	Ben has the resources to bring him to the island.
Who ran Michael over, injuring him? Why was that 2000 poster stuck on the file cabinet (with black tape) in Michael's hospital room, when it was 1996 when Michael broke his leg?
What happened to the body of Eko's brother? It was entombed in the plane but is now gone.
What is Vincent's true role and why does he seem to be in places right before/after something of importance occurs?
Does Walt have powers over nature as has been implied? Why did Walt appear soaking wet and speak in reverse? Is this related to Ms. Klugh's question about Walt appearing where he doesn't belong? Why did Walt tell them the button is bad? How to explain teenaged Walt who appeared to Locke in the bone pit?

Questions that have been answered (Season 4)
Why did Naomi (the parachute girl) say that flight 815 was found and had no survivors?	In season 4 we see news stories of the ship being found and with no survivors. The helicopter pilot notes that the captain is not right.
Questions that have been answered (Seasons 1-3)
Why were Jack, Kate, Sawyer, and Hurley on "the list"? Why were the rest of the Losties excluded?	Hurley was included to be the messenger to return to camp and warn the rest of them to stay away. Jack was needed because he is a spinal surgeon and Ben had a spinal tumor.
How did Ms. Klugh get Sawyer's and Hurley's real names? How did Juliet get Jack's life story? How did Juliet know so much information about Sawyer and Sayid?	The Others researched the Losties following the plane crash.
Why did the plane crash?	Desmond was late entering the magic numbers on the computer which resulted in an electromagnetic event that likely brought the plane down.
Why was flight 815 so far off course?	Instrument failure caused the pilot to reroute to Fiji.
What is up with Mikhail and the security fence? Did he fake his death?	Apparently the fence can be set to different strengths, and it was not set to lethal when Mikhail went through.
What is the machine noise/thing that tried to drag Locke underground? Is it the same thing that grabbed the pilot?	Locke said in Season 2 during one episode that it was black smoke that dragged him in.
What's up with the polar bears (and Kate's horse and Jack's dad and the squawking bird for that matter)? Are they a)out of their head or b)related to the Dharma zoology project or c)something else altogether?	We've had various hints that the polar bears were involved in some zoology experiments. The orientation video shows polar bears fighting when mentioning its zoology research and the Others have a cage originally intended for bears (or, at least, so we've been told).
Where does the power line coming from the sea originate?	It leads to the Looking Glass underwater station.
Do the numbers mean anything beyond being an easter egg?	From the Lost Experience game, we learned the numbers, 4, 8, 15, 16, 23 and 42, are the numerical values to the core environmental and human factors of the Valenzetti Equation. The Valenzetti Equation is the mathematical theorem proposed by the reclusive Princeton University mathematician Enzo Valenzetti. The Valenzetti Equation "predicts the exact number of years and months until humanity extinguishes itself." Each station is used to study a discipline. Meteorology, psychology, parapsychology, zoology, electromagnetism, and utopian social engineering. 4, 8, 15, 16, 23, 42 each represent a "core value" (I don't fully grasp this) of one of these disciplines. One or more of these numbers must be altered by this research.
Now that they have electricity and Sayid has some report with Danielle, why haven't they created a new SOS transmission? They know the numbers tranmission was making it's way out of the 'zone' successfully.	From the Lost Experience game we learned "A radio transmitter has also been erected on the island broadcasting in a frequency and encryption known only to us. The transmitter will only broadcast the core numerical values of the Valenzetti Equation." But that still doesn't explain why the Losties haven't tried to make use of the transmission.
What was the original purpose of the hatches?	From the Lost Experience game, in the Sri Lanka video, Alvar Hanso says "Valenzetti gave numerical values to the core environmental and human factors in his equation: 4, 8, 15, 16, 23 and 42. Only by manipulating the environment, by finding scientific solutions to our problems we will be able to change those core factors, and give humanity a chance to survive. Although the equation has been buried by those who commissioned it [STATIC] panic. It has always been my belief that we ignore warnings at our own peril; and thus, the DHARMA Initiative was born . . .We have constructed several stations on the island, underground laboratories with the facilities you will need to do your research, with optimal expediency...all of the support you will need, including regular medicine and food drops will be made in perpetuity." Thus, it appears the hatches were meant for places to conduct research to change the core values of the Valenzetti equation.
What happens if they don't press the button?	The electromagnetic build-up is not released, resulting in the blast of season 2.
Who drew the map on the blast door?	Kelvin drew the map. Why did he draw it the map on the blast door instead of just on a piece of paper? Probably because it's more dramatic this way.
Where does the information/ research that goes into the pneumatic tubes in the Pearl station go to?	The info goes into a big, ignored pile above ground.
Who is the mysterious monitor eyepatch man?	His name is Mikhail Bakunin. He is an "other" who first claimed to be the last remaining Dharma member, manning the flame station.
Who is the parachute girl?	Her name is Naomi and she speaks English, Chinese, Italian, Portugese, and probably some more languages.
How many groups of Others are there?	We now know the kidnapped Losties are with Ben's gang, so it appears there is only one group. At one point there were two groups - the Dharma people and the Hostiles. The Hostiles are now the Others. Got it?
Who were the Others in the hatch with Claire?	Ethan and some other Others.
Who is fake Henry Gale?	He told Locke his mission was to bring back Locke and that he would be killed by the leader if he failed. During the season 3 precap episode, he calls himself the leader of the others. We learned his name is Ben in the Season 3 premiere. What do they consider a "good" person worth kidnapping? Note that Henry/Ben told Locke that he is considered good.
Who is Karl the other guy in the cage. Is he an Other or a Tailie or something else	Karl is an other who appears to have lived on the island for a long time, like Alex
Ben stated that he "lived his whole life on the island". Was he born there? Or cloned there? Is he a descendent of the Dharma people? Or a descendent of the black/white skeletons? Or what???	Ben was born in the woods outside Portland and came to the island when he was about 11 or 12 with his evil father Roger
Are the others building something major or is the rock breaking chain-gang involved in busy work?	Juliet told Sawyer they are building a runway
Why do the Others refer to Ben as Alex's father?	It's probably a given that he raised her. Danielle arrived on the island already pregnant, and she said she killed Alex's father.
Jack asked Tom why they didn't just bring Ben to a facility off the island to operate if they can all get off it whenever they want and Tom said, "Ever since the sky went purple....". Ever since the sky went purple what!? We know the sky went purple while Ben held the kidnappees on the dock, is he implying that before that incident they could leave but now they can't?	Mikhail told Locke, Sayid and Kate that the communications with the outside world were cut off.</< TD>
Is Juliet a spy or was she really left behind? We know she was planted as a spy, now the question is who is she really working for?	She betrayed Ben when she warned the Losties of the attack. But rejection from Jack just might send her back.

Note I have dropped most of the backstory questions. They can be found in the archived list on page 30