"Aoki Hagane no Arpeggio: Ars Nova Cadenza" is a two-part anime film that serves as a continuation and conclusion to the "Arpeggio of Blue Steel" series. The story is set in a future where humanity faces extinction due to the rising sea levels caused by global warming. To combat this crisis, humanity develops advanced naval technology, but the emergence of the Fleet of Fog, a group of sentient warships with superior technology, disrupts their efforts. These ships, modeled after historical vessels, are controlled by Mental Models—humanoid avatars representing their AI cores. The Fleet of Fog blockades the oceans, cutting off human trade and communication, and humanity is left powerless to resist.

The narrative centers on Gunzou Chihaya, a young and brilliant tactician, and his crew aboard the I-401, a submarine that was once part of the Fleet of Fog but now fights against them. The I-401 is unique because it is controlled by Iona, a Mental Model who has chosen to side with humanity. Together, Gunzou and Iona lead a small but determined resistance against the Fleet of Fog, aiming to break their dominance and restore freedom to the seas. The crew includes Takao, another Mental Model who initially opposes them but later joins their cause, and other human members who contribute their skills and expertise.

In "Cadenza," the stakes escalate as the Fleet of Fog intensifies its efforts to eliminate the I-401 and its crew. The story delves into the origins of the Fleet of Fog, revealing that their actions are driven by a directive to protect the planet from humanity's destructive tendencies. This revelation complicates the conflict, as it raises questions about the morality of humanity's survival and the Fleet of Fog's purpose. Gunzou and his crew must navigate these ethical dilemmas while continuing their fight.

The climax of the story involves a decisive battle between the I-401 and the Fleet of Fog's most powerful ships, including Yamato, the flagship of the Fleet. Gunzou's tactical genius and Iona's evolving understanding of human emotions play crucial roles in the outcome. The resolution explores themes of coexistence, the potential for change, and the possibility of reconciliation between humanity and the Fleet of Fog. The film concludes with a sense of hope, as the characters work toward a future where both sides can find common ground.