This is probably the first of the storylines that did not have a clear resolution. The viewer got the impression that Walt was intended for something more, but for unknown reasons, the writers let him leave the island without much follow up (we see him in a couple of visions and a "flash forward" but that's it). His father, Michael, however does show back up to try to atone for some of his mistakes.
Another character that was developed and let go was Mr. Echo. A man with a violent past, he also attempts to make up for his past transgressions by helping the survivors, fighting The Others and facing down the Smoke Monster. His character is killed off and almost never mentioned again.
Along the way we learn a little more about the mysterious island, The Others that inhabit it, the DHARMA initiative, Jacob and the Man In Black/Smoke Monster. There is time-travel, the metaphysical, forces of good and evil, drama, action and mystery.
So how does this all come together? Well some say, not very well. Let's take a look. The final season is the one where we really start to see some questions answered, in a fashion. First, what is the island? What is its purpose? According to Jacob, the island is a stop-gap for a gateway to "hell". He has been protecting the island for generations and keeping the "cork in the bottle" to use his analogy. His brother is the Man In Black who we later learn is the Smoke Monster.
Which leads us to the next question. What/who is the Smoke Monster? Unfortunately, he is never given a name. His motivation is to leave the island, no matter the method or consequences. Jacob, through a momentary lack of judgement, is actually responsible for MIB's transformation into the Smoke Monster, after which MIB can take on the form of anyone who as died or is dead on the island. This becomes very important to his plans toward the end. This is because the two brothers, through a mysterious set of rules are not allowed to harm one another. MIB vowes to find a loophole which will allow him to kill Jacob and leave the island.
Next, The Candidates. Jacob is seen through flashbacks interacting with the main characters in earlier times of their lives. He speaks to them and touches them in turn, which supposedly protects them and sets things in motion that will lead them to the island. The purpose of this is so that one of them can replace Jacob as the protector of the island as he knows his time is almost up. MIB is not allowed to kill any of The Candidates himself. He finds his loophole when John Locke's dead body is returned to the island. MIB can now take on the persona of Locke, a former candidate, thereby circumventing some of the rules. He is able to manipulate the character of Benjamin Linus and the two of them kill Jacob (though Jacob is able to hang around a little longer in "spirit" form to pass the torch... more on this later).
At one point, Jack is able to leave the island with some of The Candidates. They go back to their old lives for three years but come to realize, for various reasons, that they need to find a way to return to the island. During this time the other survivors have been transported to 1974 and are forced to join the DHARMA initiative. This is a group that have come to the island to study its unique properties and try to live in a "utopian" type of community. For these characters, three years also pass.
When they are re-united, it is in 1977 and physics genius Daniel Faraday has an idea about how to change the timeline and effectively negate the plane crash and the hardships that followed for the survivors. He wants to detonate a hydrogen bomb near the source of the island's power in hopes of neutralizing it. Evidently the island was a post World War II bomb test facility and they happen to have an un-detonated bomb at their disposal. This plan appears not to succeed and we lose some characters in the process.
This is where we begin to see what appears to be a parallel timeline. I think this may be the sticking point for a lot of people as it turns out to be something completely different. In this reality, the island and Jacob never existed. The characters land at LA X safely but their lives appear to be just a little different. Eventually the characters in this existence come together and realize that they know each other and "remember" their time together on the island. More on this in a bit...
Meanwhile, back at the island, the characters have to deal with the aftermath of the failed bomb attempt. After some more hardship and some soul searching by the survivors, "dead" Jacob brings the remaining Candidates together to explain his search for a replacement and what the island represents. Jack volunteers and Jacob performs a short ritual which makes Jack "like him"(presumably immortal). This is Jacob's swan song and the survivors agree that Locke/MIB/Smoke Monster needs to be stopped.
Everyone ends up at the "heart of the island" and it's main source of power. Jack and Locke agree to extinguish its light as they both think it will serve their separate purposes. They utilize the character of Desmond as he is evidently immune to the intense electromagnetic properties of the islands power. Desmond succeeds in neutralizing the power but with disastrous effects. Earthquakes begin to shake the island and Locke runs for his getaway ship. We find that Locke/MIB/Smoke Monster and Jack are no longer immortal and they proceed to begin a fight to the death. Locke loses and he is now no longer a threat to the island. However, Jack is severly wounded and faced with the realization that he has to re-ignite the power source or the island will be destroyed and, possibly, the rest of the world.
In the mean time, the rest of the characters, minus Hurley and Benjamin Linus (who decide to stay with Jack), race to a downed plane that has been repaired and is ready to leave. They all board the plane and manage to take off just as the runway crumbles beneath them. Six people manage to escape on the plane.
Jack finds a way to save the island but he is critically wounded and does not expect to survive. He passes the guardianship of the island to Hurley who asks Ben Linus for help. Desmond also survives.
Jack wanders out to the spot where he first awoke on the island back when it all began. He lays down and dies.
In the alternate reality we find that all of the characters have gathered in a church. Jack is there as well as his father, who had passed away. We find that this reality is a type of "pocket purgatory" (I came up with that myself) and that they have created this place themselves so that they could experience a life without the island and re-unite before they move on....
This in no way cancels out the experiences that were had on the island nor is it a "Dallas-type" dream sequence. The events on the island happened in "reality" and Hurley moves forward as its' protector for who knows how many years. The characters who were able to leave on the plane move forward with their lives from there, but that is all a different story...?
Are all of the questions answered? No. It would be impossible to address the specifics of all the storylines raised. This was a big undertaking with an epic feel to it. We do not know the answers to all of the metaphysical, quasi-religious themes. But then, we do not know these in real-life either. Whether you like the ending or not; whether you found it satisfying or it left you wanting more; it was smart, thought provoking television (something that is sorely lacking these days). And, it was one hell of a ride....
