In this sentence:


I'm not sure if である is being used as the copula or the で part is used to mean "by the hands of this people" as in means of action

  • 4
    Parse it 手で、ある改造を・・・ – Chocolate Nov 7 '16 at 2:38
で  : by
ある: one(or some)

ある is just modifying 改造, like "ある日(one day)". If splitting the sentence by a space, it becomes:

当時の 人間どもの 手で ある改造を 施された

or changing its order:


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