- How did the polar bears get on the tropical island?
Taken there by Dharma - they lived in the cages that Sawyer & Kate we held in.
- How was a polar bear with the Dharma tag found in a desert?
It escaped through one of the portals off the island - and ended up in the desert like Ben & Locke when they turned the wheel
- How did Jacob's mother know about the light (its purpose and meaning)?
She mentioned her mother, who probably held the position before her, though I don't know how she got there
- Where did the black smoke come from? I know that it was Jacob's brother, but how did it get there in the first place?
It seemed to be the malevolent spirit of Jacob's brother, separated from his dead body
- How and why did Hurley know those numbers?
He heard them from a resident in the assylum when he was there initially.
- Didn't Jacks father live in a secluded house on the Island? How did he get there?
Jack's father was dead, but since his body was on the island Smokey admitted he appeared as Christian to initially lead ther 815 survivors to fresh water in the cave, and then subsequently to appear to Claire.
- How did Jacob get to America (let alone travel back in time to meet the younger castaways)? His brother couldn't leave the island, so how could he?
This was never disclosed, though he could have used the wheel like others did ?
- Why couldn't Jacob and his brother kill each other directly?
'Mother' said she had made it that way - and since she was a keeper of the island, she had 'powers' that could enable her to do this.
- How could Jack end up killing John if he... uh... couldn't kill him?
When Desmond caused the light to extinguish, Jack & Smokey (inhabiting Locke's body) ceased to be protected by whatever 'Mother' had done - they both bled after their initial skirmish to show this.
- Why was Desmond immune to radiation and how did he get his premonition abilities?
Dunno
- How did Miles get his abilities?
Dunno
- Who built the ancient society and the wheel that Ben turned (which time-shifted the island)?
Jacob's brother was seen in the dug-it well with the wheel in the background, but he never finished installing it. The well was subsequently filled in by 'Mother' but Jacob could have finished it.
- Why did VHF sound hurt the black cloud?
Dunno
- How did that pool in that temple heal people? Why didn't it heal Sayid properly?
The pool glowed similar to the Source (in the cave protected by the Keeper), so had some of the 'life' posessed by the water. Dogen said the water was not like it usually was, and so could have been posessed by Smokey so he could bring Sayid back from the dead ?
- Why was avoiding the Oceanic crash the cure-all in the finale? There were other castaways on the island (before and after Oceanic), so why was this group more important?
They didn't avoid the crash - the alterntive time line was what happened after they died (at whatever time during or long after the timescale of the 6 seasons of the show). The Oceanic group were carefully assembled by Jacob who engineered the situation so the plane would crash and they could be tested as candidates.
- Where the hell did that plane come from? I mean the big one.
The Ajira flight was used by the Oceanic 6 to return to the island, and was flown by Frank Lupidis, who conveniently survived to fly it away.
- How did John always know everything about the Island, why he could walk, what the smoke was, etc.?
The script was written that way ?
