In the aftermath of a major earthquake under Suraga Bay, Misaki (a young girl) and Toshiro (a pilot of a deep sea submarine) are rescued from a ruined city street just as leaking gasoline ignites. Reiko Abe arrives just in time, lowered from a helicopter. Scientists predict that Japan will sink within 40 years, due to subduction of a tectonic plate to the west. However, Dr. Tadokoro, who leads an oceanic scientific team that includes Toshiro, calculates that this will happen far sooner, in only 338 days. He presents his findings to Prime Minister Yamamoto who decides to create a new department for impending disaster relief assigning Saoro Takamori to cover the new duties, since of all his ministers she will take it seriously but also bring "heart" to the process.

As further earthquakes, tsunamis, and volcanic eruptions devastate Japan, the government pleads with other countries to take refugees. Yamamoto flies to China to negotiate relocations there, but his plane is destroyed by a volcanic eruption. Saoro fills the resulting vacuum in leadership and decides that Dr. Tadokoro's plan to blow holes in the disintegrating tectonic tectonic plate is the best remaining hope to not only save the people, but what remains of the country itself. Ironically it was her career that hastened their divorce 20 years earlier. Misaki becomes orphaned following her mother's death from earthquake injuries, and bonds with Reiko who was similarly rescued from, but orphaned by the Kobe quake.

Toshiro is offered a job in England and wants Reiko and Misaki to come with him, but Reiko feels bound to help others and refuses to leave. Fellow submarine pilot Shinji Yuki also turns down Toshiro's offer to work with him in England. Drillships place massive explosives deep in the crust, but the detonator is not placed properly and Yuki dies attempting to place it by submarine.