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.

Yachiyo the samurai sword carrying waitress reveals that she started carrying it to ward off bullies back in elementary school. At this time she encounters Kyoko who agrees to act as a body guard in exchange for Yachiyo's lunch. Otou Hyougo, the true restaurant manager, returns to the store after another unsuccessful search for his lost wife. His wife who has the worlds worst sense of direction got lost years ago while out shopping.