Here's a theory that's been bashing around in my head. It works if you're willing to incorporate the Many Worlds interpretation of QM (not a big jump, since we're talking about alternate timelines) and assume the writers have some knowledge of how nuclear bombs work. I'm sure physicists will hate how MWI is used here (no matter if they buy that interpretation or not), but it's hardly the worst Hollywood could dish out against science.
Each time Juliet hit the Jughead core, one of three things could happen:
2) Fizzle yield
3) Full detention
Since we're dealing with the random, quantum-level interactions within a nuclear device, we can incorporate MWI in a way that has macro-level effects. Each of the three possibilities above results in a different timeline or "World".
Although #1 may be the most likely occurrence on each hit, Juliet was going to keep hitting until something happened or she got tired and bleed to death. With successive hits, #1 becomes very unlikely.
#2 is the next most likely. You have to get a lot of fiddly details right with implosion-type bombs, or they'll fizzle. Nearly all large US bombs after WWII were implosion-types, and that would include Jughead. Since the bomb was already damaged when originally found and further damaged from the fall at the site, a fizzle yield is the most likely outcome after we eliminate #1.
A fissile yield can still make a big boom (say, enough to take out a few city blocks), but wouldn't destroy the whole Island. The result is coming into contact with the pocket of electromagnetism, which in turn needs to be periodically released, thus leading to the main timeline.
#3 would destroy the whole island, and results in the alternate timeline. The alternate timeline is truly "alternate" in the sense that it's less likely to happen than #2 (but more so than #1). In other words, it's not just a matter of point of view over which one should be considered "alternate".
My main argument against my own theory is that I'm not sure if the writers know enough about nukes to consider the difference between fizzle and full detentions. OTOH, using MWI in this way is more widely known by those writing science fiction.
Otherwise, there's not yet anything in the show that has contradicted this. There is some question if Jughead even is the cause of the split, but everything fits so far.
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