1. Why do the others take the children, and what is up with the signal fire they light before coming?
2. What is up with the black smoke, that killed the black guy. That has never been explained, only the final words of "Your next?"
3. How did the "others" move so quickly from their town to where the plane pieces crashed, when it took the actual survivors days to cover that distance?
4. What was up with that map Locke saw on the door to the bunker, that could only be seen with the black light.
5. Where are the other passengers that were taken, did they get put on the sub and sent home. Jack saw them on the other island, but it was almost a dream sequence and you could not tell if it was real or not.
6. What was up with the guys at the listening post in the arctic at the end of last season who called the bunkers guy girlfriend?
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1. I think they take the children because they are infertile. I think this is why they recruited Juliet to the island, she is a fertility specialist. Also, I think they wanted to explore Walt's 'special' abilities. Or, it could be that they took Walt so that Ben could use him to get to his spinal surgeon, Jack. These are my assumptions, not based on anything we have definitely been 'told' yet in the series.
2. That's the security system which is one of the huge unexplained items of the series.
3. We don't know, but the Others had boats. They could have used the boats or the submarine.
4. That map outlined the 7 Dharma research stations explained in the Dharma video and where they were located. And some more stuff if you're really into screen captures, blowups, and lots of theories.
5. That was not a dream sequence. That was the stewardess from the original flight, Cindy. She disappeared in season 2 on the Tailies trek back to the original survivors. The children that were stolen from the beach were with her (notice the teddy bear), and they were watching Jack in the cage when he woke up. Later in that episode, they were seen attending Juliet's 'trial' . I can't remember any other passengers that were taken other than Cindy and the children, unless they were 'redshirts' from the beach.
6. It appears that they are working for Penny, Desmond's girlfriend. She is trying to find Desmond, apparently. Penny's father works for Widmore Industries. We see Widmore and Dharma references all over the place in flashbacks, in Ben's refrigerator last week, etc. Widmore is also the company that recruited Juliet.
It has yet to be definitely explained how the groups of Widmore, Dharma, and the Others relate to each other. Although at this point it does seem that the Others were the Hostiles mentioned in a recent episode. In other words, they were hostile to the Dharma Initiative. Are the Others a group that was there before Dharma, after Dharma, or are they a subset of Widmore and some Dharma people who wanted out? Are the Others all from Widmore Industries? We don't know the specifics of these 3 groups yet, but these are some theories.