There are two meanings of innocence in Attack in the Shell 2. The first meaning refers to those puppet robots made by humans. They are innocent because they have suffered from human beings. In their eyes, human beings are gods; In the eyes of human beings, they are puppets, just human playthings, so they are innocent.
The second meaning refers to the kids who hacked their souls into machines. They are also innocent, they just want to be free. In general, it is the children and machines who are innocent, and the greedy humans who are guilty.
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