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Okay, in the Variable(I think), when Desmond was in the hospital after getting shot by Ben, Eloise comes and apoligizes to Penny because she said it was her son's fault Desmond was shot. Now Daniel has never done anything that would directly lead to Ben shooting Desmond EXCEPT convincing Jack to detonate Jughead.
I think WHH and Jughead was the incident. If Jughead hadn't detonated DHARMA wouldn't have made the computer in the hatch to negate the electromagnetism because there would be no electromagnetism to negate. So because Jughead detonated, DHARMA made the computer, which eventually Desmond was responsible to enter the numbers, which led to him not pushing them in time, which led to 815 crashing, etc., etc. So, because Daniel convinced Jack to detonate Jughead, it led up to Ben shooting Desmond.
Does any of this make sense to anyone else or am I just saying random things in an attempt to explain what's going on?
Another theory of mine is Daniel knew Jughead was the incident but knew Jack wouldn't help him unless he thought it would change the past.