The second season of NieR:Automata Ver1.1a. The year 11954. YoRHa Soldiers 2B and 9S are newly dispatched to Earth to carry out and support the 243rd Descent Operation. There, they succeed in destroying the machine lifeform core units, Adam and Eve. With the annihilation of these enemies, the Army of Humanity takes this chance to end this long-lasting war and decides on an all-out attack against the machine lifeforms. This is a record of the battles and hopes of Androids and the fate which dictates them all… As war rages on, Unit 2B and others like her question their role. Reclaiming the planet will take sacrifice, but how much more can they give and is humanity worth the cost?

When you look up at the sky, what do you see? A blue sky? Freedom? A hopeful future? The people of Tokyo see none of these. Instead, an ominous alien mothership looms overhead, engulfing the city skyscape. Three years ago, they came. The arrival of the "Invaders" sparked the greatest war humanity had ever faced—one that threatened to end the world. The Japanese government scrambled to fight the Invaders. Weapons were mass-produced, sparking controversy and pacifist movements. That day, everything changed. And yet, nothing has changed. Kadode Koyama and Ouran Nakagawa live their final days like they always have: going to school, playing with friends, and doing what any carefree high school girl would do. As they grow up, they come to learn what it truly means to be an adult, in a world where adults seem to be demons who only deceive and destroy. They come to learn the real threat to humanity is not the Invaders, but humanity itself.

In the near future, a sudden and unexplained sea rise has left much of human civilization underwater. Ikaruga Natsuki, a boy who lost his mother and his leg in an accident some years earlier, returns disillusioned from a harsh life in the big city to find his old countryside home half-swallowed by the sea. Left without a family, all he has to his name is the ship and submarine left to him by his oceanologist grandmother, and her debts. His only hope to restore the dreams for the future that he has lost is to take up an opportunity presented to him by the suspicious debt collector Catherine. They set sail to search the sunken ruins of his grandmother's laboratory in order to find a treasure rumor says she left there. But what they find is not riches or jewels; it is a strange girl lying asleep in a coffin at the bottom of the sea. Atri. Atri is a robot, but her appearance and her wealth of emotions would fool anyone into thinking she's a living, breathing human being. In gratitude for being salvaged, she makes a declaration to Natsuki: "I want to fulfill my master's final order. Until I do, I'll be your leg!" In a little town slowly being enveloped by the ocean, an unforgettable summer is about to begin for this boy and this mysterious robot girl...

On the 20th floor of the Tower, the "Regulars" who have been permitted to enter have to undertake arduous and extremely expensive tests to rank up. Most abandon hope and choose to stay where they are—but not Ja Wangnan. Wangnan is determined to reach the top and become the king of the Tower. However, he is weak and has repeatedly failed the exam, with debt collectors tailing him. In desperation, he attempts the exam one more time, only to encounter a mysterious and powerful individual: Jyu Viole Grace, a member of the crime syndicate FUG. Cursing his rotten luck, Wangnan has no choice but to form alliances with strong people, including Viole—who still refuses to be part of any team. Amid a dire situation, Wangnan must find a way to change Viole's mind to finally advance past the 20th floor, or he will never get a chance to build his legacy.