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.

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.

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.

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.