Mushi are beings in touch with the essence of life, far more basic and pure than normal living things. Most humans are incapable of perceiving Mushi and are oblivious to their existence, but there are a few who possess the ability to see and interact with Mushi. One such person is Ginko who travels from place to place to research Mushi and aid people suffering from problems caused by them.
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.
Narumi is on bad terms with her husband, Shinji, when, one day, Shinji goes missing. He comes back a couple of days later, but he seems like a totally different person, and he is now gentle and tender. He goes for a walk every day. Meanwhile, journalist Sakurai covers the story of a family that was brutally murdered, when an unexplained phenomenon takes place. Shinji Kase tells his wife that he came to Earth to invade.