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.

When a huge hurricane hits her hometown in Florida, Haley ignores evacuation orders to look for her father. After finding him badly wounded, both are trapped by the flood. With virtually no time to escape the storm, they discover that rising water levels are the least of their problems.