A secret Cold War agreement between Japan and the United States leads to the construction of Seabat, a state-of-the-art nuclear submarine operated jointly by the Japan Maritime Self-Defense Force and the US Navy. The cover story for its launch is a tragic accident: the Japanese diesel submarine Yamanami collides with a US nuclear vessel, supposedly killing all 76 crew members, including its captain, Shiro Kaieda. In reality, Kaieda and his crew survive and are transferred to the Seabat.

On its maiden voyage, Captain Kaieda seizes control of the submarine, renames it Yamato, and declares it an independent and sovereign nation. He arms the vessel with nuclear missiles, turning it into a rogue state without fixed borders, and announces his intention to sail to Tokyo to form an alliance with Japan. The United States, viewing the Yamato as a terrorist threat, mobilizes the Seventh Fleet with orders to sink it. The Japanese government is thrown into chaos, divided between those who see Kaieda as a traitor and those who see an opportunity to challenge post-war constitutional constraints on their military. Hiroshi Fukamachi, Kaiedas former classmate and the captain of the Japanese submarine Tatsunami, is dispatched to confront his friend. He tries to determine whether Kaieda is a dangerous extremist or a patriot executing a radical plan to free Japan from American dominance.

As the Yamato outmaneuvers the US Navy in a series of underwater confrontations, the geopolitical stakes escalate to the brink of war. The Japanese government, pressured by public opinion swayed by Kaiedas charismatic broadcasts, agrees to meet with him. The Yamato enters Tokyo Bay, and an alliance is formed between Japan and this new independent state. President Bennett of the United States refuses to accept this outcome, ordering a direct military attack on the Japanese flotilla supporting the Yamato. In the final confrontation, the Tatsunami is sunk while defending the Yamato, which escapes to continue its mission of challenging the worlds existing military and political order.