Although Komatsu's narrative does examine the mindsets of many different classes of society, the main plot follows a submarine pilot named Toshio Onodera and a geophysicist named Tadokoro. The story begins with Onodera taking Tadokoro to the Japan Trench in his submarine to investigate an island which has suddenly sunk below the waves. In the ensuing months, Tadokoro gathers additional evidence pointing towards the inevitable break up of Japan. Eventually, with volcanic eruptions and earthquakes occurring more and more frequently, the Japanese government is forced to take heed of his predictions and make plans to evacuate as many Japanese citizens as possible to other countries. The final chapters describe the valiant efforts of various international air and sea rescue forces who struggle to save as many people as possible as the archipelago breaks up and sinks. The novel is structured as 30 chapters and an "Epilogue", with the 30 chapters grouped into six sections.
Synopsis
ONE: The Japan Trench
- A man named Toshio Onodera runs into an old friend named Rokuro Goh at a Tokyo train station. Goh complains that some unexpected disturbances have caused major setbacks in his construction project, the Super Express line. Onodera tells Goh that he is going to be investigating an island which has recently mysteriously disappeared.
- Onodera arrives at the ship Hokuto, which will carry the submarine Wadatsumi to the former island site, where Onodera will pilot his employer's sub. He greets the geophysicist Tadokoro who asks about the depth limit of Onodera's sub.
- While heading south, the Hokuto comes across a small volcano erupting in the middle of the ocean. They also experience a small tidal wave shock caused by an undersea earthquake in the nearby Ogasawara (Japan) Trench.
- The Wadatsumi is moved to a new ship, the Daito Maru. There, Onodera attends a meeting in which eyewitness accounts are given from survivors of the sinking island. They report that the ocean floor in that region had sunk almost 600 feet in two and a half days.
- When the Daito Maru reaches the former site of the now-sunken island, Onodera takes Tadokoro and another scientist named Yukinaga down to the ocean floor in the Wadatsumi where they discover unusual ripple marks and volcanic rock projections on the ocean floor.
- The next day, the explorers visit the Ogasawara Trench and descend to a depth of 24,000 feet. There they detect massive ruts in the ocean bed, leading to a turbulent underground mud current. This causes Tadokoro to become agitated.
TWO: Tokyo
- Back on shore, Onodera's boss Yoshimura takes him to a bar where he advises him to get married, as that will help his chances at getting a promotion. Onodera later meets a hostess named Mako who intrigues him.
- Yoshimura brings Onodera to a private party at a beach side villa where he meets a passionate woman named Reiko Abe. However, their lovemaking is interrupted when a volcano erupts on Mount Amagi and a tidal wave approaches the shoreline.
- After Mount Asama also erupts, the Japanese Cabinet decides to schedule a panel of earthquake experts. Onodera visits Tadokoro, who seems very upset about something. Yukinaga soon arrives and tells Onodera that Tadokoro has been withholding information about the strange markings they had seen in the Japan Trench from his foreign sponsors.
- At the earthquake panel, Tadokoro theorizes that Japan might sink, although his colleagues think him mad. Later, Tadokoro is brought before an old (but apparently well-respected and wealthy) man named Watari who asks him about the strange migratory behavior of swallows this year. Tadokoro tells him that he is working on the answer to that question. Soon, at Watari's prompting, the Cabinet begins financing Tadokoro's research. While Onodera vacations in Kyoto, a massive earthquake strikes, causing 4000 casualties.
THREE: The Government
- In the following months, Tadokoro establishes a new research center in Harajuku to work on "Plan D", a research effort designed to confirm his fears about the possible sinking of Japan. He believes this could occur in anywhere from 2 to 50 years, but without additional funding he cannot be more precise.
- Months later, Tadokoro urges his small team to make faster progress. Because the Wadatsumi is unavailable, he secretly purchases a foreign-built submarine for his research in the Japan Trench, taking pains to avoid drawing press attention to his efforts.
- The night before Onodera is to start dives using the new foreign sub, he goes to a bar and fears for Tokyo's future. By coincidence, he runs into Mako.
- As the months pass, the Plan-D team continues mapping the Japan Trench. Tadokoro learns that, due to mantle convection, a drastic tectonic event will soon occur, sinking Japan in a relatively quick, apocalyptic event. As he explains this to his staff while out to sea, a massive earthquake hits near Tokyo.
FOUR: The Home Islands
- In Tokyo, two members of Plan D, Yamazaki and Yasugawa, are caught in their collapsing headquarters during the quake. Yamazaki somehow survives and notes that fires are burning throughout the city. He wonders if the Cabinet will survive this disaster.
- Onodera and Tadokoro return to Tokyo and in the morning and learn that the earthquake, fires and tidal waves have already killed 2 million people.
- The members of Plan D soon calculate that Japan will very likely be destroyed in two years. They inform Watari, who remarks that he has noticed a change in the flora and fauna surrounding his mountain retreat. He tells Onodera to obtain the services of a scholar named Fukuhara in Kyoto.
FIVE: The Sinking Country
- In a meeting at the Prime Minister's residence, party members consider protecting the PM from falout in case Plan D's predictions turn out to be false. The PM, however, fears for the worse and wonders if he is up to the challenge.
- As winter arrives, protests begin breaking out and the press begin to suspect a cover up. Onodera runs into his old employer Yuki, who chastises him for abandoning his old company to join Plan D. Onodera decides to have Yuki join Plan D.
- More eruptions occur along the Fuji volcanic belt. A mysterious foreign sub begins shadowing Plan D's base ship. Japanese representatives begin approaching other countries in the hope of quietly relocating large numbers of Japanese to other continents.
- Watari consults Fukuhara and the other scholars he has had brought to his compound. They provide him with possible outcomes for the future of the Japanese people after Japan sinks. Most plans involve relocation, but one suggests they do nothing and merely succumb to their annihilation. Watari heads for Tokyo with the plans.
- In Osaka, Onodera's brother tells that, because the region has been sinking 1 inch every day, his job opportunities have been shrinking, and he is debating moving to Canada. Onodera encourages the idea, but regretfully withholds the truth about Japan's oncoming fate.
- In February, about a year and a half after Onodera's first sub dive with Tadokoro, Plan D's simulations suddenly indicate that Japan will break into two pieces and then sink within ten months. The Prime Minister tries to maintain order amongst his party leaders amidst internal panic. International financial institutions begin to suspect the truth and start cashing in Japanese bonds. Rumors of Japan's destruction begin to reach the Japanese public. Onodera reunites with Reiko Abe in a passionate interlude and they impulsively become engaged.
- An American scientific group shocks the world when it reports that a major tectonic event will strike Japan within a year. This forces the Japanese government to quickly announce the truth to their citizens. Onodera makes plans to go to Switzerland with Reiko, but Reiko becomes caught in the destruction when Mount Fuji erupts. The Japanese archipelago slowly begins splitting along a north-south crack.
- Stunned into silence by the Prime Minister's announcement of Japan's impending dissolution, the people of Japan at first simply try to get back to their homes. The Pacific coast begins sinking at the rate of 9 feet per day. Nonetheless, most citizens try to remain calm and put their trust in the government.
- The members of the UN begin debating approaches and criteria for distributing refugees from Japan amongst their countries.
- Various national governments offer to help, but they also make plans to take advantage of the power vacuum in the Pacific. Other countries fear the influx of Japanese refugees.
- On April 30th, a massively-unprecedented earthquake strikes the Osaka-Kyoto region. By this time, a rate of half a million Japanese a day are being evacuated from the archipelago. Nonetheless, time runs out as Japan begins breaking up into various pieces.
- As parts of Osaka go underwater, civil unrest grows in Japan. Yukinaga and his colleagues at Plan D continue to record the break up of the archipelago.
- Having joined dangerous rescue operations since the loss of Reiko, one day Onodera descends from a helicopter to a mountain top to try and rescue some climbers. One of them turns out to be Mako. While trying to form an escape plan, the volcanoes around them erupt.
EPILOGUE: The Death of the Dragon
- As Japan continues to break up, a ""Japanese Miracle" occurs in which 65 million are evacuated over 4 months. By July, only the Hokkaido airport remains in operation. Tadokoro remains with Watari in Japan until the end. By September, the archipelago has all but disappeared. Yukinaga and the remainder of his team sail to Hawaii in their research vessel. Onodera wakes up to find Mako near him and hazily recalls being rescued by a helicopter. As they continue in a train towards an unknown destination, Mako tells him a story about the birth of her grandmother's people on Hachijo Island. She also tells him that she can no longer see Japan outside the window.