SudoSu
A high school student.
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Safety net. And even if Hiruzen is seemingly better here, he isnt totally kind and not the only potential threat. There are also many other things the organisation can help him, from small stuff like funds to larger ones like eliminating someone who is a threat to fuijin but he cant act himself. And most importantly, it makes the plot better.... Overall, Ithink Fuijin is being real and not dark.
You could explain black lightning with science linked to that of this world. Tho I doubt Sato would have known it unless he was decent at chem(a bit over HS lvl). Tho if u need/want it, I will explain it in a over simplified version(im bad at explaining)- When atoms bond with each other(especially covalently) the attraction b/w the atoms after meeting specific criterion create distortions, when energy, generally photons or electrons enter it, the distortion and subsequent emission leads to colour/light of different wave length. More the distortion, more is the light captured. So chakra bonds might just absorb all the photons, giving the lightning black color, tho considering how lightning works this is neigh impossible.