Takanashi Souta, lover of all things small, is recruited by his tiny sempai Taneshima Popura to work at the family style restaurant Wagnaria. There he meets his new co-workers and begins to learn about their many quirks.

Souta meets Mahiru, who suffers from Androphobia, the fear of men. The rest of the staff sets them up to share shifts in a suicidal, for Souta at least, attempt to cure Mahiru.