After the end of the One Year War, a man named Led Wayline was recruited to serve in the Federation Survey Service. One thing is though, Led has no idea who he was. But as the time passes by, he gets some dreams of his ties with a Zeon pilot named Johnny Ridden.

Due to global warming and rising sea levels of the early 21st century, humanity lost much of the Earth's landmass. At the same time, fleets of powerful sentient ships of unknown origin armed with advanced technology and weapons, known collectively as the "Fleet of Fog", mysteriously appeared and easily vanquished the world's naval forces. The Fleet of Fog impose a worldwide naval and aerial blockade, and thus preventing humanity from traveling across the seas.

Seventeen years after the battle, for some reason, Gunzou Chihaya and his crewmates aboard the I-401 and the personification (Mental Model) of the I-401, Iona, started fighting the Fleet of Fog...