There are two schools of thought on Season 6. One, it provided a confusing back story of the island and Jacob. Two, it provided nothing to the original story lines. The former would have just ended the series with the cliffhanger of Season 5, with Juliet pounding a rock on Jughead. That would have had just as many outraged viewers and unsolved mysteries. The latter would have just squeezed the key Season 6 bits into the last episodes and forgot about the sideways world filler. So the series would end with Jack dying in the bamboo grove with Vincent, while the last of his friends flew overhead for the last time.
In one respect, that last sentence would have made a more powerful and true ending to the series than the happy reunion in the purgatory church.
What happened on the island in Season 6 was masked by the confusing sideways parallel universe arc. The key resolution of the survivors's stories was on the island.
Jack accepts the role of guardian from Jacob, but he does not feel any different.
The big mission was to go into the Heart of the Island, where the unique electromagnetic energy was strongest, and to "reset" the island. This is like the Hatch fail safe operation key that Desmond used to destroy the Swan. Since Desmond survived that re-set, he was the chosen one to re-set the island for good. But despite the guardianship role and Flocke's presence, no one knows exactly what is going to happen. Flocke believes the island re-set will free him and the island will fall to the bottom of the ocean. Jack hopes that the re-set will destroy the smoke monster and free his friends.
Once at the cave of the Heart, Flocke ties a rope to a tree while Jack ties the other end around Desmond. Desmond tells Jack that this - killing Flocke and destroying the Island - doesn't matter because once he goes into the cave, he'll go to another place where they can be with the ones they love, where they never have to see the island again, and where a happier version of Jack exists. (This is the foreshadowing of the sideways church reunion, but can be just a way of saying that everyone will meet up again in heaven some day.) After saying that maybe there's a way he could bring Jack there too, Jack says he already tried that and that he found there are no shortcuts or do-overs; that whatever happened, happened and that all of this matters. The three men enter the cave.
Jack and Locke enter the cave and begin to lower Desmond into the brilliant abyss. Flocke remembers John Locke's memories of Jack and he, looking at Desmond down in a hole in the ground, lightheartedly commented on their bickering on whether or not to push the button. Jack cuts him short. "You're not John Locke; you disrespect his memory by wearing his face, but you're nothing like him." Jack insists that John was right about almost everything, and wished he got to tell him this when he was still alive. Flocke says John wasn't right about anything and that when the Island drops into the ocean and Jack drops with it, then he will realize this. Jack suggests they just watch and see who turns out to be right, and the two look down the waterfall now that Desmond has reached the bottom. (This is the big theme of science vs. faith playing out for the last time.)
Desmond reaches a chamber below after passing skeletons. He finds the Heart, a glowing pool, filled by a small waterfall, with an elongated stone with ancient hieroglyphs engraved on it at its center. He enters the water as electromagnetic energy emanates from the Heart. Desmond is clearly in pain, and his nose bleeds. Jack and Locke hear his screams. Desmond reaches the center stone and lifts it, like removing a giant stopper in the center of the pool. The stream from the waterfall stops, the electromagnetic force recedes, the light goes out, the pool dries up and there is a red hot glow emitting from the center. Desmond screams "No!" Flocke says to a very worried Jack: "It looks like you were wrong." Flocke says goodbye and leaves as earthquakes begin to wrack the Island.
Jack chases Flocke out of the cave in a fit of fury, punching him in the mouth and jumping on him when he falls. Flocke bleeds from the mouth. MIB is shocked to see he's bleeding. Jack sees the blood and says, "It looks like you were wrong too." Jack's hands move towards Locke's throat as they struggle. Locke finds a rock and hits Jack in the head, and gets up and runs off as Jack becomes unconscious.
On the Hydra Island beach, the outrigger reaches the shoreline. Miles calls Ben, who is sitting with Sawyer, Kate, and Hurley. Miles informs him they're going to fly off the Island and that they should get to Hydra Island now. Claire emerges from the bushes and holds Miles' group at gunpoint and shoots into the sand. Through the radio, Kate hears that Claire is there. Claire assumes Flocke has sent them there to kill her. To convince her this isn't the case, Richard tells her they can go home and be free of Flocke. He invites Claire to join them but she refuses and leaves.
The predicted wild storm arrives and the earthquakes continue. Ben notices a large tree beginning to fall and realizes it will crush Hurley. Ben pushes him out of the way and the tree falls on Ben, pinning him. Sawyer, Hurley and Kate can't lift it. Sawyer says Flocke was right, the Island is going down. Miles radios Ben. Kate finds Ben's radio in the mud. Miles tells Kate that Frank is fixing the plane and they should get over there quick smart. He also tells Kate that Claire is around but won't come. Sawyer uses a fallen tree branch as a lever to try to free Ben. Ben says he knows how they can get to Hydra Island - that Flocke has a boat.
On the main island, Flocke stands on the cliff above the cave, looking at Libby’s husband’s boat anchored a short distance offshore. Before he can make it to the boat, Jack catches up to him, mad as ever. Flocke turns around and the two face each other for the final showdown. (This goes to the theme of black vs. white; good vs. evil.) Flocke draws his knife and they run at each other across the uneven ground. Jack leaps at Locke and they fight as the storm rages and cliffs disintegrate.
Flocke drops his knife, but during the struggle he picks it up and inflicts a fatal wound under Jack's rib cage. As he tries to finish him off, Flocke tells Jack that "he died for nothing." Just then, Kate shoots him from behind; she had "saved him a bullet." (This final act of defeating MIB was Kate, not the island guardian, in such a way that Jacob was destroyed not by MIB but by Ben.)
Jack struggles to his feet, but another quake shakes the Island and Flocke says Jack is "too late" just before the rumbling stops. Jack kicks him off the cliff to the rocks below, and MIB, the Smoke Monster, is apparently dead.
Kate holds Jack, who looks at the knife wound in his side. Jack says "I'll be fine, just find me some thread and I'll count to five.” This is what he said the first time they met in the jungle after the crash. Kate sewed up Jack's wounds, which may be symbolic of threading their lives together. Sawyer, Hugo and Ben arrive and as Kate tells them that it's over, the Island rumbles again and Sawyer says "Sure don't feel like it's over."
Ben tells the group that Frank and the rest are leaving, and if they are going to catch up they had better get to the boat and sail to Hydra island quickly. Jack says that whatever Desmond turned off, he needs to turn it back on again. But he says that if people are going to leave they need to get on that plane. Kate tells him that he doesn't need to do this, but Jack is adamant that he does. Jack wishes Sawyer good luck.
Ben passes Sawyer the radio saying that if the Island is going down then he is going down with it. Hugo refuses to climb the rickety wooden ladders and tells Jack that he is with him. Kate and Jack share a tearful goodbye - they have a final kiss and declare their love for each other. The island continues to shake uncontrollably. Sawyer calls Frank, who tells them he is going to leave while there is still ground to leave on. Sawyer and Kate jump off the cliffs and into the sea. They swim out to the Elizabeth.
Frank fires the plane up. Kate and Sawyer swim ashore to Hydra Island and find a disconsolate Claire sitting on the beach. The Island continues to disintegrate. They hear the Ajira warming up. Claire says to Kate that she won't come because the Island has made her crazy. Kate offers to help her and they all run for the plane. Frank prepares for takeoff and doesn't hear Sawyer's plea on the radio for him to wait. Just then they make it to the runway, and Kate, Sawyer and Claire climb aboard.
The plane takes off as the runway disintegrates.
Hurley helps Jack as they return with Ben to the Heart. Jack tells them he is going down alone and makes it clear that he knows he will not survive. Jack explains to an overwrought Hurley that this is what is supposed to happen. Jack tells Hugo that it is he who the Island needs, that his job was to fix the Heart but after that it should be Hugo. Jack tells Hugo that he believes in him. Hugo agrees, but only till Jack returns. Ben finds an Oceanic bottle and Jack fills it from a leftover pool of water from the previously active stream and gives it to Hurley. After Hurley drinks, Jack tells him,
Ben and Hugo lower Jack into the Heart. Jack finds Desmond and carries him back to the rope. Desmond wants to return the plug but Jack tells him he has done enough and he needs to go home to be with his wife and son. Desmond asks Jack what will happen to him. Jack says that he'll see him in another life, "Brother." (This ties up the connection between pre-island Jack and Desmond when they first met on the stadium steps. It would seem that destiny would unite their lives in the near future.)
Jack lies exhausted in the empty pool but a trickle of water starts flowing and then the light starts to return. Hugo and Ben haul on the rope and find Desmond on the end of it. Below, Jack sobs with relief as he is engulfed in the light. (Some may speculate that this should have made Jack into an immortal smoke monster.) Ben and Hugo are with Desmond. Hugo takes in the idea that Jack has gone. Ben comforts him by telling Hugo that he did his job. Ben tells a frightened Hugo that he can do his job as the island's new island protector by doing what he does best: taking care of people.
Hugo asks how he can do things like helping Desmond to go home when people can't leave the Island. Ben says that that is how Jacob ran things and that maybe there is a better way. Hugo asks Ben for his help, saying he needs someone with experience. Ben says he would be honored.
But Jack is not really gone, as the final scene on the island is Jack in the original bamboo grove.
How he got to the bamboo grove is another mystery. One theory is that Jack never left the bamboo grove in the first place; that it was all his dream. Another theory is that after re-corking the island, saving it from destruction, the light cave transported him to this place as it was the end of a portal. It was so that Jack could see his friends fly away; so he could pass in peace and move on.
You could have just ended the series without the Hurley assuming command immaterial plot point.
But this sequence as the true finale would have made pretty clear that the ultimate sacrifice, one's own life, is needed at times to save others. Dying alone meant that others could live.
We would know that the island's magical powers over life and death have a valve, the rock cork, that once disturbed can cause great riffs in time and space. It has its own fail safe mechanism if released, which is to destroy the planet (extinctions are part of planetary evolution). This changed the immortals into mortals. But rebooting the island is also possible as Jack did - - - not to save the world (he was unaware of the consequences) but to save his friends.
Eliminate the sideways story line and one gets a better picture of the island mythology, and a better end to the show.
