Season 1: Character and Island Introduction
A plane crashes. Every character has a complicated back-story that often inter-twines with others on the plane. The island has many strange features. Season 1 ends with lots of questions.
Season 2: The Hatch
The castaways live in a bunker of sorts and learn about the Dharma Initiative (hippies doing experiments back in the 70s) and there's an escalating conflict with The Others.
Season 3: The Others
We don't learn this yet, but The Others are Jacob's tribe, with the job of protecting the island. About 25 years earlier, The Others killed the Dharma Initiative and took over their houses. The castaways are captured by The Others.
Season 4: The Freighter
The leader of The Others, Ben Linus, has an arch-nemesis: Charles Widmore. Widmore sends a freighter of mercenaries and scientists to the island. The mercenaries are sent to capture Ben Linus. The scientists are studying the island. The mercenaries kill Linus' daughter. The scientists end up joining in with the castaways. The castaways are escaping from the island to the freighter when the freighter explodes. About the same time, Linus moves the island. (It vanishes.) A few castaways were in a helicopter on the way to the freighter... those 6 got off the island.
Season 5: Time Travel
When Ben Linus moved the island, he sent either it or the remaining castaways on the island jumping through time. Eventually, the castaways manage to stop the time-travel jumps and they are stuck in the 1970s working with the Dharma Initiative. Meanwhile, off the island, the ones who got off the island decide to go back to the island to try to save their friends. When they crash on the island again in a different plane, some of them jump back in time to the 1970s while others stay in present day. The 1970s people decide to set off a nuclear bomb to change the future so that the original plane never crashes. That doesn't work, but they do all time-travel back to the present again.
Season 6: Finale
We are left wondering about whether the nuclear bomb worked, as we watch two seemingly parallel universes: the original story plus a new story where the original flight never crashes (i.e. the 'flash sideways'). In the last episode we learn that the flash-sideways is actually the fist stage of the afterlife. As the castaways make connections with one another in the alternate universe they "wake up" and remember their real lives. In the finale they move on to the next stage of the afterlife, which is not revealed.
We also learn some about the island mythology, but not as much as a lot of people wanted. The island is the "source" of everything. There is a protector (Jacob) and an embodiment of evil (the smoke monster, aka the Man in Black). Jacob is protecting the island and keeping the MiB from leaving the island. Rules prevent them from harming one another. Through a very complicated (and clever) plan, the MiB tricks Ben Linus into killing Jacob for him. Jacob manages to pass on his mantle as protector of the island to one of the castaways. The first castaway protector kills the MiB and then immediately names another castaway as the new protector before dying from the wounds he suffered in the fight with MiB.
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OR THE LONGER VERSION:
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2000 or so years ago ship crashes on island. Several people survive, but one is separated, a pregnant woman.
She's found by "mother," another woman who presumably had crashed on the island. They both spoke latin, so they were somewhat contemporary to each other.
The castaway woman is killed by mother after she gives birth to twins, Jacob and MIB.
Jacob and MIB grow up with mother, eventually MIB leaves and lives with other castaways for 30 years after learning of his origins from his birth mother's spirit.
Eventually Mother has to slaughter the castaways and ruin MIB's donkey wheel works. In anger MIB kills mother, but then is cast into the light by Jacob and becomes the smoke monster.
1800 or so years pass...
About 140 years ago Jacob realizes that MIB needs to be killed. His brother sat down for a chat with him and told him that he wanted to kill Jacob and eventually he'd find a way.
Because Jacob is so clever, he uses the rules against his brother. He orchestrates the Losties to arrive to disrupt the organized society that Jacob has built.
MIB thinks that he's taking advantage of the chaos of the Losties and is able to find a loophole in the "rules" so he can off Jacob and get the heck out of here. The problem is that MIB is no Jacob, he's a kind of side effect of a mistake of Jacob. So he doesn't have as big of a picture of the island and what it is all about.
So MIB falls for Jacob's trap, trying to nudge Locke to leaving the island so he can come back dead (why he's anticipating this isn't clear) so he can then claim Locke's body. He then proceeds to infiltrate the others and is able to get Ben in to see Jacob so Ben can stab him.
Jacob wanted Ben to stab him and get killed, because he still had mojo even after dying and finish the trap. The thing is that when MIB took Locke's body he had become diminished to some degree. He was locked into Locke's body or the smoke form. It's kind of like how the Balrog's in the Lord of the Rings were dimished Maria, spirits that had become so corrupted by Melkor that they could only exist now in demonic forms.
Jacob then tells Widmore to come back to the island, put up a good show of trying to fight MIB, but when he gets caught to tell MIB what he needs to do to switch the island to the "off" setting.
Jacob meanwhile sets his final pieces in place, getting Jack to accept his role as the "fixer" for the island. He passes on his power of guardian to Jack and then finally passes on, hoping (I guess) that it'll all work out and he didn't just end up destroying the universe.
Jack can't be messed with directly now since he's the new Jacob. So rather than get into a useless fight MIB just has Jack come along so they can lower Desmond into the hole to flip the switch.
When Desmond hits the switch by uncorking the island the rules suddenly turn off. Now MIB is mortal again, he can't turn into smokie and so he runs. This eventually leads to the slugathon fight between Jack and MIB.
Kate, who seemed insignificant to MIB with her name crossed out, ends up gunning down MIB and then he gets shoved off the cliff.
Finally, the island is cleared of this taint that Jacob had created. MIB was a super being who's resentment and anger had festered on the island far too long and made it likely that at some point the whole world would come to an end because of his super powers.
Jack then goes back and turns the island's switch back to the "on" position.
Losties die at various times. Jack just a few hours later, meanwhile those that flew off the island live whatever lives they have and then eventually die out in the regular world.
Hurley (who Jack passes the torch of guardian onto) and Ben (who becomes Hurley's assistant) presumably are immortal, but of course they too pass at some point, handing off their roles of protecting the secret fire at the heart of the universe to someone else.
Once everyone is dead they get shunted to the sideways universe which is a kind of purgatory. Being outside of time and space, it could wait for all of the losties to arrive, even if it might take a very long time since Hurley and Ben could have lived for a very long time. Eventually though they all get there and at that point they have to just link up with each other, remember what had happened, find joy in reunions in the afterlife. Once they were all gathered and settled, they could finally move on to whatever eternity has waiting for them.
Ben needs a bit more time in Purgatory, so he hangs back, he needs to be the father he never was able to be to Alex. Anna Lucia likewise has a way to go before she realizes where she's at and is able to accept her life and death. Eloise Widmore likewise is still so wracked with guilt over killing her son that she needs more time with him before she can move on.