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Despite the confusion over the hospital scene, Naota does have a brain. The X-ray picture shows the N.O. portal inside his brain, which absorbs X-rays, creating the illusion of an empty space. N.O. works because of left and right brain interaction, so there must be a brain if N.O. is working. Haruko was just badgering Naota when she told him that he doesn’t have a brain.
