"Arpeggio of Blue Steel - Ars Nova" is set in a world where rising sea levels have drastically altered the global landscape, and humanity faces an existential threat from the Fleet of Fog, a mysterious armada of sentient warships with advanced technology. These ships, which emerged suddenly, have cut off maritime trade routes, crippling human civilization. The Fleet of Fog operates under the control of a central intelligence known as the Admiralty Code, and their ships are equipped with powerful nanomaterial-based weaponry, making them nearly invincible against conventional human forces.

The story centers on Gunzou Chihaya, a young and resourceful naval officer, who becomes the captain of the I-401, a sentient submarine modeled after a World War II-era vessel. The I-401, also known as Iona, is a Mental Model—a humanoid avatar representing the submarine's consciousness. Unlike other Fleet of Fog ships, Iona defects from the Admiralty Code and allies with humanity, offering her advanced capabilities to aid in the fight against the Fleet of Fog. Gunzou and his crew, including his childhood friend Shizuka Hazumi and the stoic engineer Sojiro Kyouhei, embark on a mission to challenge the Fleet of Fog and reclaim the seas for humanity.

As the crew of the I-401 engages in battles against other Fleet of Fog ships, they encounter additional Mental Models, each with distinct personalities and motivations. These include Takao, a heavy cruiser who becomes fascinated by Gunzou's tactics and develops a rivalry with Iona, and Hyuuga, a battleship Mental Model who initially opposes the I-401 but later joins forces with Gunzou. The interactions between these characters explore themes of identity, loyalty, and the evolving relationship between humans and artificial intelligence.

The narrative delves into the origins of the Fleet of Fog and the Admiralty Code, revealing that the fleet's purpose is tied to a deeper, enigmatic agenda. As Gunzou and his crew uncover more about the Fleet of Fog's true intentions, they must navigate complex moral dilemmas and strategic challenges. The series combines naval warfare, science fiction, and character-driven drama, with a focus on tactical battles and the evolving dynamics between the human crew and their sentient ship.

"Arpeggio of Blue Steel - Ars Nova" balances action and introspection, presenting a story that explores the consequences of technological advancement and the potential for coexistence between humans and artificial intelligence. The series concludes with an open-ended resolution, leaving room for further exploration of its world and characters.