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The Maritime Self-Defense Force submarine Yamanami collides with a U.S. nuclear submarine, crushing all 76 people on board, including its CO, Shiro Kaieda. Hiroshi Fukamachi, CO of the MSDF diesel submarine Tatsunami, becomes suspicious of the accident and analyzes the recorded data of the collision.

The Seabat, a state-of-the-art nuclear submarine hijacked by Kaieda, surfaces in front of the U.S. Seventh Fleet, which has assembled to sink the Seabat as it is considered a terrorist threat. There, Kaieda makes a startling declaration.

Fukamachi's diesel ship Tatsunami arrives in the area, where the operation is in a standstill after Kaieda's declaration. In an attempt to stop Kaieda, Fukamachi boards the Seabat.

Kaieda finally begins to combat the U.S. forces. Three nuclear submarines of the Seventh Fleet close in on the Seabat. Chief Cabinet Secretary Wataru Unabara heads to a summit meeting with U.S. President Bennett.

A Japan-U.S. summit meeting is held, but neither country concedes to the other's claims. Meanwhile, the U.S. Third Fleet launches an anti-submarine missile at the 2nd Maritime Self-Defense Force convoy led by Commander Numata, which has been dispatched to escort the Seabat.

After the battle with the U.S. Third Fleet, Kaieda arrives at Tokyo Bay to conclude an alliance with Japan. The Japanese government announces to the public a series of events that began with the top-secret Seabat Project.

Kaieda appears at the meeting. The alliance negotiations between Japan and the independent nation of Yamato are reported to the world. As soon as the talks are over, President Bennett identifies the Yamato as a terrorist organization and orders its destruction.

The MSDF floating dock Southern Cross, which is carrying the Yamato, begins to sink under the attack of the U.S. forces. The Yamato tries to escape before the ship sinks. The Tatsunami, that was put at risk to escort the Yamato, begins to sink.