Here’s my theory. The first third of Season 6 will follow two timelines. One of them will be the alternate timeline. The alternate timeline will be revealed to be a “What If” scenario created by Jacob to teach the Losties the terrible consequences of their alteration of time if it had actually worked. The trick is if they want to leave this timeline, they will leave it together and the characters find themselves in situations in the timeline that will make that a bit difficult. The other timeline will be the timeline taking place after Jack and the others wake up from their alternate timeline experience and what they do from that point on while Richard, Sun, and the others deal with the Fake Locke.