Nagisa Yamada is a cold and withdrawn middle schooler living in a rural town in the countryside. Her mother works part-time jobs in her late father's stead to support Nagisa and her brother Tomohiko, who is a "hikikomori"—someone who is also extremely reclusive. Nagisa aspires to be a soldier for the Self Defense Force to finance both her and her family's needs.

One fateful day, a transfer student by the name of Mokuzu Umino transfers into her school. She immediately garners the classes' attention for being the daughter of a renowned singer and her cute appearance. Claiming to be a mermaid, she seeks out Nagisa, the only person who seemingly harbors no interest toward her. Mokuzu declares that a storm is coming, and she wants Nagisa to be her precious friend. Otherwise, when the storm comes, Mokuzu will go back to the sea, turn into foam, and disappear.

Satougashi no Dangan wa Uchinukenai: A Lollypop or A Bullet follows Nagisa and Mokuzu, as the pair bond over real-life issues in hopes of a better world.