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Cut/n/paste save. I am going to edit the first post.

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I've always wanted one place to go to get a summary of what we still don't know. I will keep this post updated as the season progresses and questions are answered and new ones are asked.

Please keep this thread spoiler free.

Setting Questions

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.

Where is the island located?

What is the black smoke?

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?

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.

Why do trees explode/vanish?

Where did the food drop come from?

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?

How does Ben and/or Jacob cure cancer?

What causes the pregnant Other women to die? Is it 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.

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).

Does the squawking bird actually say Hurley's name?

How did an enormous slave ship get to the middle of an "island?"

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.

Why do the props in the hatch change? Is this meant to indicate passage of time? (Check out this link found by JPGramma for photos)

What is the significance of Widmore? Pen Widmore was Desmond's girlfriend.

Who was Michael communicating with on the computer?

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? Will the next video host have Wax in their name?

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.

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?

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.

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?

What is the "magic box" described by Ben?

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?

Who is the parachute girl? Her name is Naomi and she speaks English, Chinese, Italian, Portugese, and probably some more languages. Since Naomi is not working for Penny, who was she working for and how did she get the Des/Penny photo?

Why did Naomi (the parachute girl) say that flight 815 was found and had no survivors?

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.

The Others

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.

Why do The Others claim they can't go to the Losties camp themselves ? It could be as simple as...they are lying and are trying to manipulate Michael to do their dirty work..just to see if they can push him that far. But...still nothing is for certain.

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?

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.

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.

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.

Ben seems to have had a relationship with both Juliet and Colleen. What's the story there?

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?

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 was Juliet trying to impregnate her sister who appeared to be battling cancer?They thought that Rachel's cancer was gone at that point.

Why was Ethan in Juliet's building? Did he visit her sister?

What is the significance of the x-rays of the 26 year old woman with the uterus of a 70 year old. Who was the subject?

Did Rachel's cancer really come back or was Ben lying to Juliet just to get her to stay on the island somewhat willingly?

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.

How did the Others get back the boat that they gave to Michael & Walt?

Why did Mikhail (the Russian flame station guy) kill Ms. Klugh? Or was that faked like Mikhail's security fence killing?

How/why has Juliet's shoulder been dislocated 4 times?

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. Who knows?

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?

The Losties

Why is there so much apathy and lack of communication among them? This seems to be less of an issue in season 3.

Ana Lucia

What was her purpose for being in Australia? She went to Australia with Christian as his bodyguard.

Who was on the phone that interrupted her drink with Jack?

Bernard

Charlie

Why didn't Charlie go look for Locke and Eko when he found out they weren't back at camp? (the place blows up, his buddies are missing and he just sits by the fire????)

Christian

Is he really dead?

Who is the daughter he was trying to see in Australia? Claire, as revealed in Par Avion.

Cindy

What happened to her?She was kidnapped with the rest of the Losties by Ben's gang and seems to have been brainwashed.

Claire

Was told by a psychic that she must raise the baby. Then he backtracked and arranged to send her to America to give up the baby for adoption. Did the psychic foresee the crash?

What did the psychic foresee that caused him to tell her she must raise the baby herself?

Why does Claire's baby daddy art work look so much like that "art" on the island?

Desmond

Where did he go when he ran away from Jack and the others? On his boat.

Why was Desmond naked when he woke up in the jungle after the blast?

How did Desmond know about Locke's rescue speech before it happened? Prophecy? Time wrinkle?

Did Desmond really travel back and forth in time after the implosion or was he subconsiously dreaming about past events all jumbled up while unconscious?

Hurley

Jack

How did Jack's father die? He died of a heart attack brought on by alcohol poisoning.

How did Jack end up in Australia?Jack went to Australia to bring his father's body

Where or how did he become such a crackshot with a gun?

What happened to the body of Jack's dad?

How could Jack fall out of a breaking up airplane traveling hundreds of miles an hour and land unhurt in some trees?

How/why did he get the tattoos? He got the tattoo by forcing the Thai tatto chick to do it, then was subsequently beat up by her brother and his gang. Who knows why? I don't care.

Who did Sarah leave him for? Was she really pregnant? Was she lying?

Why does it seem Jack was the only one thrown really far from the plane?

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?

Jin

Kate

What happened to Kate to get her running in the first place? She blew up her mother's house to kill the mother's boyfriend after she found out he was her biological father.

Where exactly did Kate end up after the plane crash? We first see her coming out of the jungle.

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.

Libby

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?

Locke

How did Locke's legs get injured? Locke's father pushed him through a window in a highrise.

Was Locke inspecting a house for Sayid's Nadia? Video evidence suggests he was.

What was the secret he whispered to Walt in the pilot of the show? Was it the secret about his paralysis?

How the hell can Locke predict rain?

What was in that wacky paste he put on Boone's head?

How did Locke's dad get on the island?

What happened to Locke's hand? (it was bandaged when he said goodbye to Kate and left with the Others) Cooper bit it

Michael

What happened to Michael after he ran off after Walt? Why is he now killing people? Michael was captured by the Others that live in yurts and have a heavily guarded hatch. He spent a week there being questioned then they released him to orchestrate the release of Henry Gale and to bring back Jack, Kate, Hurley and Sawyer in return for Walt's freedom.

Who ran him 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?

Was Michael's story about the primitive others and their hatch true? Partially - he probably believed that was how they lived, but he knows he is bringing the four Losties back to a trap.

Why did the Others take Michael's blood? Was it just to determine paternity or do they have another use for it too?

Mr. Eko

How did Eko end up in Australia and why was he going to America?

What did Eko do after he was left behind when the drug plane left with his brother? It appears he took on the role of his brother as a priest but was not yet redeemed.

Was Eko really on flight 815 or did he just run out into the water after the crash? He was most definitely on the flight, as we saw in ?

Was Charlotte telling Eko the truth at the airport or was she doing as told by her "psychic" father?

How did Eko's brother's plane end up on the island?

What happened to the body of Eko's brother? It was entombed in the plane but is now gone.

Rose

Sawyer

Who conned Sawyer's parents? In other words, who is the original Sawyer?. Tom Sawyer was revealed to be Cooper, Locke's evil daddy.

Ben and his gang know Sawyer is a con man and turned it around to con him. Why?

Was Sawyer conned by the Cassidy? If so, who is Clementine. Cassidy met up with Kate and admitted that she still loved Sawyer and was having his baby.

Sayid

Is Nadia the same person Locke was inspecting a house for? Video evidence suggests he was.

How did Sayid learn to speak English so fluently?

Sun

Did she have an affair?Yes, she had an affair with Jae that was discovered by her father.

Now that we know she had an affair, who is the father of her baby? Juliet claimed that the baby was conceived on the island, making Jin the father.

Did Jae jump or was he pushed? If so, who pushed him?

In Season 2, when Sun and Jae were having lunch together he told her he'd met an American woman at Harvard and was going to go be with her. What happened to that relationship? Who was the woman? Will she have any importance to the story later?

Vincent

What is Vincent's true role and why does he seem to be in places right before/after something of importance occurs?

When Jack, Kate, and Charlie are going for the cockpit, why did Vincent just sit there in the bushes watching them? Wouldn't a normal dog go greet them?

Walt

Where is Walt? We know he is with Ms. Klugh, but don't know exactly where they are holding him. Walt and Michael are now off boating

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?

What sort of tests did Ms. Klugh and her gang have Walt perform?

Why did Walt tell them the button is bad?

How to explain teenaged Walt who appeared to Locke in the bone pit.

Other Losties

What happened to the children and "good" people taken from the tailies? They were kidnapped by Ben's gang and seem to have been brainwashed.

Yes, I think that is when she mentioned the numerous relocations.