I think it does its best telling the story that was contained in the original manga (which had not concluded yet upon the release of the movie), but I also think the reason why a number of people are confused about the story, is that it tries to condense so much of the manga into 90 minutes. I would in fact recommend anyone who liked the movie to check out the manga, because it follows mostly the same beats of the anime, but expands upon the world and the characters significantly. At any rate, both the anime and the manga are powerhouses in their respective mediums.
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clarity of thought before rashness of action