Faraday: "I can negate the energy under the Swan."
Kate: "How can you destroy the energy?"
Faraday: "I'm gonna detonate a hydrogen bomb."
Faraday warns against drilling to release the energy, but blowing a bomb would make an even larger hole to release the energy. The key word is "NEGATE". Not blow up the Swan site, not "plug up" a hole, but NEGATE the energy itself.
If the energy under the Swan is of one polarity, one would need a large force of the opposite polarity or phase to cancel it out or "negate" it.
A regular plutonium core wouldn't do that, but one from the opposite phase reality or dimension would. Faraday figured a way to get the Jughead from one dimension and bring it to the other.
The strong magnetic (opposite polarity) field produced by the hatch via Desmond, opened up a hole from the one reality, to the opposite polarity version, and the Oceanic 815 from that polarity dimension entered into the other one, so now there are TWO Oceanic 815 planes in that world.
One on the island, and one on the bottom of the Sunda Trench that is ALSO the REAL Oceanic 815.
But now in the OTHER polarity reality, (where the Oceanic 815 came from) there is NO Oceanic 815. If any plane is "fake" perhaps someone put a fake one in that dimension.
The island has pockets of energy that we have been told "have an almost LIMITLESS energy" that if harnessed correctly will give the ability to "manipulate time" The properties of the island "have created a kind of casimir effect." Allowing the DI to "conduct experiments in both SPACE and time." "four-dimensional space"
The island heals people that are from the opposite polarity reality. (high power Magnetic Therapy) But if Ben was switched as a child (stolen from the other side as a replacement for the Ben that was shot by Sayid) then Ben is in the SAME reality as the island, thus the island can't cure him when he has cancer.
This also explains why Jack's apendix needs to be removed and why the island can't cure him, because he ALSO is from the same polarity as the island. We know this via his tatoo:
"he walks amongst us, but he is not one of us"
If Jack was not one of them BEFORE the crash, then when he crashes on the island, he is now actually in his correct world, unlike the rest of the survivors! And thus why he needs his appendix removed, because the island can't heal him either, just as it couldn't heal Ben.
Meeting with Isaac the healer in Australia, Rose was told that he was unable to help her. It wasn't that she couldn't be healed, but rather the energies present at that place weren't right for her.
But she COULD be healed if the strong pocket of magnetic energy was of the opposite polarity, like on the island which is in the opposite polarity universe.
This also explains the pregnancy problems. If the fetus is formed OFF the island, it is the same polarity as the mother, but if the fetus begins ON the island, it is a person that is of THAT reality, which is opposite polarity of the mother who came from the other reality.
Claire got pregnant OFF the island, her baby is no conflict to her on the island as they are two people from the same polarity. Those getting pregnant ON the island, create a new life (person) that exists in a different polarity than they are, thus the body rejects it.
The Jughead from the opposite polarity reality "NEGATED" the energy, thus the hole never opens for the Oceanic 815 to fly through it, and it lands at LAX. But in the other reality, unless the same thing is done, we have a problem, and the two realities won't stay in sync and we will still have people "LOST" in the other reality.
"Magnetic Therapy" and it's concern for the polarity of the magnets facing the body, is not unlike the healing properties of the island to those that come from the other reality.
The island seems to have swaped from one reality to the other, as opposed to the rest of the planet.
Because of the opposite polarity of the alternate reality, the North and South poles are also opposite. That Earth would be upside down in relation to ours, so that exiting directly from the island, you would end up at the ANTIPODE of the other, such as in Tunisia.
Sayid noted that the compass points differently than where it should in this reality. Perhaps East is West, and North is South.
And perhaps night is day and day is night. How often have we seen a scene in daylight, and suddenly when we get back to that same scene, it is dark night?
Naomi landed wearing a helmet with oxygen & parachute.
In one reality, Naomi, who was sent to the island by Widmore, originally crashed on the first of two helicopters sent by the Kahuna. She died in that crash out in the ocean.
In the other reality, Naomi, who was sent to the island by Penny, flys over the island in a high altitude aircraft, and lands far inland on the island in a tree.
Thus why we see a helicopter crash way out in the ocean, but she lands a fairly good day's hike inland hanging in some trees.
We know there was only one copy of the photo from the street vendor that took the photo, and the writers made sure Desmond broke up with Penny right after the photo was taken and he had possesion of it, so that we would know there were no other copies of it. Desmond took it with him to the island. At least that's how it happened in the one polarity dimension we were shown. In the other polarity dimension, Penny seems to have the photo, and makes a color printout of it to give to Naomi.
Before arriving on the Island, Naomi was with Matthew Abaddon and Naomi commented that she believed there may be survivors of Oceanic Flight 815 on the island. Abaddon reassured her in a stern manner that there were no survivors.
Now skip ahead...
After waking up, she asked Hurley where she was. He informed her that she was on an island with survivors from Oceanic Flight 815. She replied that wasn't possible as the plane had been found with no survivors.
In one time line, (or dimension) Naomi is surprised to learn there are survivors of the island which she heard from TV that all were found dead. When she comes back the second time, she knows (and tries to tell Abaddon) that survivors are on this island.
She was wearing a dark tinted visor. Why wear this at night?
If her lung was punctured the night before, (if this was the same Naomi from the helicopter) by the time Desmond and his team found her, and Mikhail tried to revive her the next day, hours after walking inland, she would have been dead for hours and could not have been revived. This Naomi had just landed.
Mikhail claimed she had thanked him for saving her. Her actual words were "eu nao estou so" which is Portuguese for "I am not alone".
Naomi tells Sayid that her search and rescue team was hired by Penelope Widmore, although she had never met Penny herself, to search for Desmond.
Yet the Naomi that died in the first helicopter crash was with the rest of the Kahana team working for CHARLES Widmore, not Penny.
The next day Naomi tells everyone about the radio phone and tells them it's not important that the world thinks they're dead. Also note that the radio phone is slightly off the settings from the Kahana crew of the other dimension and her phone has to be reset to slightly different settings to match theirs.