first off let's start with Senku's:

1. military weapon- probably the most credible. Also labs out in the jungle are a fun trope seen in anything. We also have some of the villagers on treasure island who posses the weapon
2. virus- this probably wouldn't have been as fast and is somehwat discounted by what's happening on treasure island
3. aliens- could be and that they left their stuff behind...then again they could have left stuff behind
My addition:
Lost technonlogy- South and central America are known for have quite a few lost civilizations. What if the whole thing was set off by accident by tripping the wrong thing in some old lost temple? Any humans who were left could have easily just adapted what was there for our current arc.

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