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.

Takanashi is visited at work by one his 4 sisters. Hiroomi the assistant cook attempts to blackmail the staff of Wagnaria so that he won't have to work. At the same time it becomes apparent that Satou the head cook has a thing for Yachiyo the head waitress.

Takanashi spends some quality time with his four quirky sisters; the boss, the drunk, the writer and the manipulative. Each in their own way is reliant on Takanashi to keep their family in order. White Day has arrived and Takanashi gifts Mahiru a bag of hair pins. This is the first White Day gift she has ever received. Later he runs into her on the street worried that she might attack some random male while walking around he escorts her home. On the way they run into his eldest sister Kazue. Mahiru get flustered and admits to "assaulting" Takanashi on a regular basis.

The girls decided to take a trip to the hot springs which will be the first time for Mahiru. Takanashi concerned about the fate of the male guests at the hot springs goes as well. In the end the entire staff ends up going only to be so late that the hot spring is closed by the time they arrive.

Takanashi and Mahiru go on their "date". The staff of the restaurant fearing for Takanashi safety concoct an elaborate plan to have him cross dress so that Mahiru would think of him as a girl and not hit him. As the date comes to a close Takanashi comes to realize his true feelings for Mahiru and Mahiru receives the compliment of her life.