Miyuki Amaya (Kasumi Arimura) belongs to the sailing team of manned submersible research ship 6K (Shinkai 6500) at JAMSTEC  (Japan Agency for Marine-Earth Science and Technology). She dreams of piloting the 6K. Her father was a pilot and a researcher, but died from a disease. Miyuki Amaya’s purpose is to research the deep-sea because her father told her about the deep-sea when she was little. Now, she is a cadet of the pilot. 

One day, Miyuki Amaya has a chance to get on the 6K, but she finds a tape in her father’s locker. The tape contains horrific images. The image is of an unknown giant creature and pilots that were left alone in the deep-sea. Her father's last moments are contained in the images. The images are totally different from she imagined as the beautiful deep-sea. Miyuki Amaya is now horrified. Can she safely return from the deep-sea?