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So the big question is whether or not Jack and Co. changed the timeline and had Oceanic Flight 815 actually land at LAX. I'm going to give my two cents on the topic.
I was always against the Losties changing the future because of the many paradoxes involved (the main one being if the survivors never crashed on the Island, then they were never there to prevent the Incident) but now I have a new theory that ties in with the Jacob and his Nemesis story. The timeline that we have been watching for 5 seasons has been an alternate timeline, and we will start to see the real timeline, which is the survivors never having crashed on the Island. We will see that someone connected with Jacob's nemesis brought the Dharma Initiative to the Island, which started the chain of events that brought the survivors to the Island. If Dharma had never came to the Island, then the survivors would never have come either because it was Dharma who messed around with the electromagnetic properties of the Island and made it unstable, causing the crash of 815. The Widmore Corporation and the Hanso Foundation have been shown to be linked, so I believe that Widmore had a big hand in bringing Dharma to the Island. I think in the "war" between Jacob and his Nemesis, the Nemesis found out that by altering the course of time and bringing a plane full of survivors to the Island, including the late great John Locke, he could eventually impersonate Locke, infiltrate the Others and kill. Oceanic 815 crashing on the Island was the result of an altered timeline. But Jack and Co. have now tried to set the timeline back where it belongs. But where does this leave us for Season 6?
I don't think Jack and Co. exactly did as they thought they would. I think the detonation of the atomic bomb halted the rise of the electromagnetic energy, but the electromagnetic energy is unstable and damaged, so every 108 minutes it will rise too high and have to halted by pushing a button. Sound familiar? I think that if Jack and Co. hadn't been sent back in time to detonate the bomb at the Swan, the Island would have been done for. The energy would have kept building up (the first system failure!)and caused some serious shenanigans on the Island. Jack and Co. caused the Incident, they didn't prevent it. This is the Nemesis covering his steps...I'm not going to pretend to be able to connect all the dots of the Nemesis' plan, but did he have anything to do with Ajira 316 landing on the Island a few days before the Incident? It's obviously not a coincidence. It was the Island bringing them to that time, but what force of the Island, Jacob or his Nemesis, was responsible? I believe that again, it was the Nemesis.
Season 6 will show us what happened on the Island after Juliet detonated the bomb. They will either get sent to the present (hence Jacob's "They're coming") or they will get sent to yet another fun time on the Island, maybe the ancient civilization's time. But we will get "flash sideways" to what would have happened if 815 had landed at LAX. But they can't base an entire season around erasing the events of the 5 previous seasons. And the writers would probably want a new interesting device to show flashes of the characters, as you can't simply have flashbacks and flashforwards all the time. Will the timelines eventually converge? Who will win, Jacob or the Nemesis? Is my theory completely wrong? We'll have to see in February.