Ohmygoodness don't tell me that, here too, people are going to start screaming harassment, molestation, abuse of power and rape???
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Well, right now it is a story about abuse of power sexual harassment. Calling it rape is obviously going too far. Also, we don't really know what Indou's thinking, only that this is clearly making her really uncomfortable. If she decides she's fine with it, then you can't really call it harassment anymore.
To repeat myself--and yet and yet. As we've pointed out from the first, this series poses some real conceptual problems in trying to match up real-world historical and cultural values.
By the standards of contemporary Western society, you're quite right.
By the standards of the Japanese military of the early 20th century, there's functionally no such thing as "abuse of power" by a military superior to a subordinate (well, technically there was, but it would be quite a ways from anything we've seen here). And trying to triangulate what "sexual harassment" would look like in that context is rather daunting.
By the standards of this specific imagined storyworld, the jury is still out. We know that something like a "maiden" relationship exists, and Ooba suggests that there may be something problematic about it, but we don't know its actual status--are such relationships approved of by the authorities, are they a kind of student-body institutional tradition on the down-low, how common are they, etc.? And what's with Kagami's rejection of the term in light of her behavior toward Indou?
One thing that makes this different from other series set in such parallel storyworlds is that I don't get the feeling that information is being arbitrarily withheld, but that we'll learn how this world works along with Indou.
(This is all stipulating that I do not consider fictional works to be primarily guidebooks to real-world moral behavior submitted for our approval or disapproval.)