Miyuki Amaya becomes the first female pilot of the Shinkai 6500 in Japan. The Japan Agency for Marine-Earth Science and Technology (JAMSTEC) had put effort into her first submersible across the organization. Miyuki's father had also been active as a brilliant pilot and researcher of JAMSTEC, but died of illness without fulfilling his life ambition. Miyuki is intent on discovering herself in the deep sea that her late father had told her about when she was a child. However, at one time, she finds shocking footage from her father's locker of the last submersible that he had allegedly piloted, and is assailed by fear.