This is a part of how I understand a thing about the swan. I hope this can help you to better understand or discover new things. I will explain, in another post, how the following gibberish can explain the cabin mysteries. Well, to begin, we know that the wheel (at the orchid) is related to time travel. We also know that the bomb explosion at the swan created a jump in time. Thus we know that the swan and the orchid are correlated. The theory is that, in the core of the island, always happened a stable electromagnetic oscillation every 108 minutes. When the swan pocket as been drilled, the system has been modified and the oscillation was stopped leading to some sort of instability, the one, at high amplitudes, creates a strong gradient force upon metals. After the pocket was drilled, and the bomb exploded, the chinese man Chang understood that his son had jumped again, and thus that the swan was correlated to the orchid, so the dharma understood that they had to inverse the oscillation themselves and they settled a device in the swan, connected to the orchid so that with a synchonized signal each time the amplitude becomes a threat (every 108 minutes), they could inverse the oscillation and take a 108minutes break. That's why the computer is connected to the network, to send the inversion signal order to the orchid. But the dharma also had an alternative issue : opening the pocket of energy once for all (discharge) although they didn't know what would be the consequenses, that's why they advised to do that discharge only in last resort. They put the trigger (such a trigger don't need to be synchronized with the orchid) in a box and secured it with a key. When desmond turned that key, the pocket discharged in the sky, but now with an empty pocket the system swan-orchid was broken, and from now on causing the wheel to malfunction forever. When ben turned the wheel, this was after desmond turned the key, and the wheel gone crazy, jumping some guys in time (the ones who had been once in there life (past or future) to the orchid), with a high probability arrival near the departure date. All the time flashes were handled by the 2004 wheel, the wheel based on a non-periodic oscillation, that caused them to jump randomly with the same probabilities. After that, john turned it, but this time the wheel he turned was part of a none damaged swan-orchid system because the discharge hadn't occured yet, so the crazy time travels were fixed by the good sequence of events in the island core. They lived 3 years stuck in the pre-incident period, and then, when the bomb exploded, the energy of the blast interacting with the orchid-swan system made a course correction and sent the guys back in the time where they were supposed to be. Please let me know if this is in contradiction with the show

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