This is my theory. It plugs quite a few of the plot holes, and I'm sure you will agree it is pretty spot on...
That light was Jesus. When they pulled the plug, they pulled the plug on Jesus which would have let the whole Island get sucked into Hell. MIB then lost his special powers (until Jack put the green crystal from Krypton back in), which is how Lois Lane managed to shoot him. With Jesus plugged back into the main power lines, all was ok again.
Jacob was an angel, and Hurley and Ben became angels at the end, helping Lost souls on the island that doesn’t exist.
Walt was actually an incarnation of Satan and was trying to create a portal between Hell and Heaven from where he was going to unleash vampire polar bears onto the world. He was attempting to gather his horde in the desert, where nobody lives, prior to launching his cunning attack. He recruited a load of lost souls and formed the Dharma institute to help with his satanic aims. The clue is in the name d-HARM-a, with the D and A standing for Desert Assault.
When the Angel Jacob dropped his brother down Jesus’ hole, he fell into Jesus. Jesus sucked out his soul and then essentially ‘farted’ it back out as a Jesus Fart Monster. It could kill anyone who had failed the test for redemption. It basically tidied up people who had failed by either sending their souls to Hell, or forcing them to end up roaming the Island forever as a dead soul.
Clare and Sayid were punished more on the island, and were turned by the Jesus Fart, because they had been baddest in the real world, and so had harsher tests (Torturer and Baby Seller/Australian – Sayid was tortured and Clare had her baby stolen/was forced to live in The Bush).
Jim Robinson was also a lost soul, who was trying to be reunited with Scott and Lucy’s mum, who died when Lucy was young. What they didn’t show was at the back of the church Jim being reunited with his long lost wife, his mum-in-law Helen Daniels and Bouncer, who the Losties had mistakenly called Vincent. I think Daphne may also have been there with Jo Mangle’s wife! It was definitely Bouncer though. Vincent is a stupid name for a dog. It’s like calling your dog Barry or Dave!
‘Time travel’ was possible on the Island as time didn’t physically exist. Ancient Egyptian lost souls had discovered this and built the wheel and various other things to manipulate the metaphysical island, and it’s links with Purgatory. Only people who had passed the test could actually return to purgatory via Plane, Submarine, Boat OR ‘dying’ on the island by any means except the smoke monster (or committing suicide selfishly – both game over for your soul). You couldn’t die otherwise – the Island wouldn’t let you.
The Island constructs ‘tests’ based around people’s past experiences and memories, hence Hurley’s numbers being in there, Locke’s father, etc. The Island is actually ‘St Peter’ from the bible, letting people in/out of Heaven. The real name of the island is St Peter’s Island, and that was who the big statue was of. If you translate the hieroglyphics, they all say things like ‘St Peter’s Island’ or St Peter’s Place, or ‘Heaven’s Gate’ etc. I know because I translated them with my own eyes.
Once tests are passed and people get to ‘Purgatory’ they are essentially waiting to pass through to Heaven, where the free beer and hookers are. Ben had to wait as he still hadn’t done enough angel-ling to make up for all his badness during his life and testing on the Island. Locke forgiving him probably knocked a few hundred years off his wait though. He may also have been waiting for someone else from the Island to join him? Maybe he got a new ‘daughter’ that he didn’t kill this time around.
Michael totally failed. Not only was his son actually a version of Satan, but he murdered and betrayed people in a selfish attempt to leave the island. (Note: Not all these people are lost souls. Some are just ‘AI’ contructs to help with the tests. They spawn fairly randomly.) Michael remains as one of the whispering dead souls in the woods.
Rose was the Oracle and Bernard was The One, but they played a passive part in this version of the Lost Souls construct.
Mr Eko did look like his soul would be saved, but his conversion back to Catholicism did for him. God does NOT like child molesters.
He was doing fine up until he found his religion again, the fool.
Just to clear things up. Penny was also dead, but in purgatory trying to find Desmond. There is some degree of interaction between purgatory and St Peter’s Island, but I’m not going to explain the metaphysical concepts here, as quite frankly, you wouldn’t understand them. That is all you need to know.
When Charlie wrote NOT PENNYS BOAT on his hand, he was actually writing TAOB SYN NEP TON, but the fool forgot to write it backwards! ‘Taob Syn Nep Ton’ is Ancient Egyptian for Your Sins Kill You, which was a cryptic message to Desmond that in order to escape, he had to be good.
I think that about covers everything.