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.

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 takes the day off work to take care of his sick sister. The staff attempts to function without them and deal with Mahiru's fear of men with no male server to deal with the male customers.

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.

Otoo returns to Wagnaria once again this time bringing with him a new waitress, Yamada Aoi. Aoi tells a "tragic tale of woe" to which Takanashi responds that she is a liar. Reluctantly he ends up training Aoi in how to be a waitress. As the day progress she tries to assign the various staff members into a fake family structure.

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.

The source of Mahiru's fear of men is revealed to be a plan concocted her father. Mahiru's father finds out that Takanashi gave her a gift for White Day and visits the restaurant to meet him. Mahiru, afraid that he has come to make her quit working there ask Takanashi to pretend to be a girl. Takanashi mans up and wears a skirt.