This is not a spoiler, but it is my theory, but not the unreasonable theory of someone who doesn't understand how narrative television storytelling works. Most theories I read are ludacris and fit nothing in the form of intelligent or rational storytelling. Anyways, I think I have a pretty good handle on someone of the larger things that are going to happen, so I wouldn't read this if you don't want to be spoiled.
The claiming, or infection, referenced now with Sayid has nothing to do with the dark water. It has to do with him dying. He died because of the dark water in the spring, but he was infected BECAUSE he was dead. The smoke monster has the ability to CLAIM people that are dead, reanimate them, twist them. This is what happened to Rousseau's team, and this is what happened to Claire. Claire died when the freighter team attacked New Otherton. She died and came back before Sawyer found her, just like Sayid died and came back. When Christian took Claire with him, it was to join him, because she was infected, and so was he. That's why his body has been missing all this time. Christian sometimes is a ghost, but sometimes he is real.
The Smoke Monster is recruiting the perfect army . . . an army of people that his enemies will not kill. Kate, Hurley, Jack, and Jin could conceivable kills Others without much remorse, but how is Kate going to kill Sawyer, who the monster will try and recruit next episode. How can Jack bring himself to kill his sister? This may be why Flocke wanted Sun to follow him for what amounted to apparently no reason. I think, before Iliana dropped the real Locke at Sun's feet, he was planning on recruiting her too, to counteract with Jin.
There will be a war, but the war will be between the original 815's, both on different sides. This will lead to the most tragic and saddest moments of the series as friends kill friends, and family kill family. The smoke monster is gaining an army that can double as psychological warfare.
Now, I don't know what the candidate mystery is, or adam and eve, but I do believe that all of the 815ers will die. They will all perish, leaving only two people alive, Jack and Flocke. There will probably be a last conversation between the two, and the tone and subject matter will echo every conversation the two have had about faith, purpose, and the island. Jack will do something sacrificial. He'll die from his actions, but it will cause something incredible to happen. It will be this action that causes the island to sink at some point in time between 77 and 04. It will also stop the monster.
In the sideways world, we will see the lives of the 815's interconnect in various ways, moving and uplifting, mirroring similar events on the island (Sun and Michael's friendship, Hurley falling for Libby, Sawyer settling up with Anthony Cooper, Locke being able to walk, Charlie meeting Claire, Sawyer meeting Juliet, Sayid finding Nadia and attoning, etc). There will be negative consequences to the 815ers never crashing, but there will be lots of positive resolutions too. Ultimately, most of the lives will end up happy, or at least happy according to the individual character.
This is the ultimate end of the story, but we won't understand this till the very end when Jack makes the sacrifice that tops the smoke monster and sinks the island. At that point, after the glory of that climactic moment, we will flash to white, and Jack is looking out the window, and everyone is alive in 2004. The end is the beginning, or the beginning of season 6. The island, submerged underwater, never caused the plane to crash, thanks to Jack's sacrifice, and everyone carries on to find their ultimate destiny, to which we have already seen in the flash sideways. We, as the audience, will have seen the great emotional destiny and ultimate joy that the most if not all of the 815ers will find, and it will all resonate in the fact that it is real, and they will be okay as we leave the island world behind and we spend the last minutes of lost in Oceanic 815 visiting the images of our favorite characters as they sit, still lost in their lives, but alive, and on their way to s! till great challenges and even greater rewards in their lives.
I wouldn't even be surprised if the last shot is a close up of Jack's eye as it closes.