First of, I have to say this is definitely not my theory but it's what I was able to get to from reading the blog by LOST IN TIME and the comments from users such as Dretzle, Sean Sheep, DaemonRising and others. I made a sketch that might help in explaining what I have reached, and I would like to share with you all.
What I am trying to say is that there is an infinite number of timelines that always exist. They are all supposed to lead to the same events as long as nobody interferes with them. The only possible way to interfere with a timeline is through time travel and this makes the person interfering a VARIABLE as Faraday liked to call it. Since you can't change the past and Whatever happened, happened...you have to make those changes in a different timeline from the one you exist in. The losties time flashed to a new timeline or the FST when they were in 1977...they influenced a bunch of people and detonated a hydrogen bomb. All this had many changes in the future of this timeline such as the plane never crashing (because the swan was never built) or jack having a son or sawyer becoming a cop. They then flashed back to their own timeline where no changes had occurred. This then explains where the FST came from, what caused all the differences and why it is important. This theory can be used to explain other stuff. You can say that MIB is from a different timeline and he was able to flash into the original timeline we have seen. If he leaves, there will be changes causing everyone to "cease to be." However this is a different story and I would rather not get into it.
I hope you understand what I meant and sorry if the picture is not clear.