In Japan in the year 1600, at the dawn of a century-defining civil war, Lord Yoshii Toranaga is fighting for his life as his enemies on the Council of Regents unite against him, when a mysterious European ship is found marooned in a nearby fishing village.

Ford Brody, a Navy bomb expert, has just reunited with his family in San Francisco when he is forced to go to Japan to help his estranged father, Joe. Soon, both men are swept up in an escalating crisis when an ancient alpha predator arises from the sea to combat malevolent adversaries that threaten the survival of humanity. The creatures leave colossal destruction in their wake, as they make their way toward their final battleground: San Francisco.