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Mina is just doing her job. Idt she'd let anything bad happen to Kafka even if he is a kaiju. They would most likely want to do tests on him since this is the first time a human could transform into a kaiju, but I'm sure they'd do it in proper/humane ways. They could use Kafka as a special soldier against the other kaiju.
Started reading this bc of The Anime Man. This is such a good read! Can't wait for more updates, esp since this chapter ended on a cliffhanger!