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A lot of information was revealed in the most recent episode of LOST, "Happily Ever After". Finally, some light has been shed on the true nature of the Flash-Sideways Timeline (hence force referred to as FST) and how it relates to the Original Timeline (OT).
For a moment, let's assume that the FST exists solely because of "The Incident" as depicted at the end of Season 5. Up until this point, the entire series of LOST had existed in one timeline, or one reality. Certain characters have travelled through time, but they have stayed solely within the same timeline they always had.
"The Incident" changed this. The detonation of the Atomic Bomb created a split in time, and a second reality; the FST. Therefore, prior to "The Incident" there was no FST. The entire history of the world before 1977 is exactly the same in the OT and the FST. The split caused by the detonation of the atomic bomb gave us two timelines.
In the original timeline, the bomb was never detonated and events unfolded as we've seen in Seasons 1 through 5. In the FST, the Island was destroyed by the atomic bomb and sank to the bottom of the ocean (or somehow ended up under water). Characters lived out their lives as if the Island never existed and, most importantly, Oceanic 815 landed successfully in Los Angelas in 2004.
It's become quite clear in "Happily Ever After" that Desmond is the link to uniting these two timelines. He is the one character who has successfully been able to send his consciousness through time and space and experience other timelines. It could be said that Desmond exists not as two people in two different timelines, but as one person across both timelines. Other FST characters, such as Charlie and Daniel, have been shown to have had visions of the OT, but can't fully travel between the timelines as Desmond can.
Desmond, realizing that he is happier in the OT with Penny and his son, is assisting Widmore in the OT while trying to convince the other Oceanic 815 passengers of this split in time. It is my belief that through some event yet to be shown, Desmond will successfully unite the timelines whereby the consciousness of all FST chracters will be transported to the OT in 2007. Thereby making the events in Season 6 on the Island (2007) the future of both the OT and FST.