Flying Phantom Ship

Returning from a happy fishing trip, Hayato Arashiyama and his father witnessed a traffic accident, whom they identified to be chairman Kuroshio (owner of the shipyard Hayato's father worked in) and his wife. Helping Kuroshios taking shelter from a thunderstorm in an abandoned Western-styled mansion, a mysterious figure with a skull mask haunted them, calling himself the caption of a phantom ship. A few days later, a giant robot calling itself a messenger of the phantom ship, appeared from nowhere and attacked the seaside city, killing many civilians including Hayato's parents. Hayato's father told him a big secret before drawing his last breath. To avenge his parents, Hayato joined the volunteer defense force organized by chairman Kuroshio, yet he stumbled upon more and more surprising and horrible secrets.

Synopsis from Anime News Network