Haven’t thought this out too much, but here’s the gist of it:
Richard Alpert, Charles Widmore and “Jacob” were passengers on The Black Rock, and for some reason, are unable to die. John Locke and Michael were also passengers on the same ship, but again – for an unknown reason, they are in some sort of time loop or reincarnation cycle so that they don’t realize who they are. We know Michael can’t be killed. And it looks increasingly like Locke can’t either – he survived as a premie, despite the odds, he fell 8 stories and survived, and was shot by Ben. Locke may even BE Jacob, but it’s irrelevant, the point is, the survivors of The Black Rock are duking it out for control of the island. Not sure what to make of Christian Shepherd just yet – he may be another passenger on the Black Rock, but I think it’s more likely he’s just the form Jacob is currently taking, or possibly the form future- or past-Locke as Jacob is taking. Also, I don’t think Ben is a passenger. If he was, he would not be so helpless now. No, he knows the backstory, and realizes “his time” is not only over, but it never really existed.
I suspect it will eventually be revealed that Widmore is both Magnus and Alvar Hanso.
I’m just piecing this stuff together on assumption, not proof. But I think we’ll see some serious stuff revealed soon, because these types of reveals won’t explain much, and yet, will explain everything. Is Locke’s mother “Emily” the same woman as Ben’s mother “Emily”? Is Christian Shepherd more than a hallucination? Does “moving the island” mean moving it geographically? Or will all of this be revealed to circumnavigate the bendiness of time?
Because that’s where all of this is going. Time is the key, and if time is pliable and actually bent, nothing is certain. It explains how Richard Alpert is everywhere, he can go back later and be right on time. It’s how Ben is so powerful. It’s eventually going to explain Adam and Eve, Christian’s empty casket, Desmond’s flashbacks, etc.
It’s all very exciting.