A fleet of unmanned ships, called the Fleet of Fog, equipped with super advanced weapons and technology suddenly appeared all over the world. Mankind didn't have the capability to face such a fleet and so was defeated in a devastating naval war. This resulted in mankind being driven out of the seas and losing their ability to travel the seas. Years after this devastating naval war, Chihaya Gunzou and his friends are aboard the I-401, a former Fleet of Fog submarine. Together with the I-401's mental model, Iona, they take on the Fleet of Fog.

Note: The first three episodes received an early screening at a special event on 21 September 2013 at Cinem@rt Shinsaibashi in Osaka and on 22 September 2013 at Cinem@rt Shinjuku in Tokyo. Additionally, the final episode received an early screening at a special event on 21 December 2013 at Odaiba Cinema Mediage in Tokyo. The regular TV broadcast started on 8 October 2013.

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Sequel: Gekijouban Aoki Hagane no Arpeggio