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.

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.

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.

Aoi becomes curious about Hiroomi's secret life and drags Popura into stalking him, despite the fact he is completely aware of it. Later, Popura tries to get Sota to treat Mahiru nicer. Tired of Jun's teasing, Popura tries to get revenge on him which does not go to plan. Meanwhile, Aoi acts very clingy around Otoo after he comes back from his recent trip.

Whilst out shopping for some more cream, Kyōko and Yachiyo end up meeting Otoo's long lost wife, Haruna. As Yachiyo debates whether to tell Kyōko about her, she disappears again. As Yachiyo feels guilty about it, Mahiru learns about Jun's one-sided crush on Yachiyo and starts feeling sorry for him, leading Sōta to believe she has a crush on Jun. With some support from Jun, Yachiyo apologises to Otoo after he returns and cheers up.

Whilst Popuar is pleased to finally reach the report sheet, Sōta is horrified by the thought of her growing taller. Whilst talking about the future, Aoi ends up turning a statement from Popura that she might have to leave Wagnaria some time in the future to a rumour that she is actually quitting, which she spreads to the other staff members. As the staff have their concerns over this, much to the annoyance of Maya the bird, Popura is confused by their weird reactions to her. After Maya helps Popura with her worries, the truth about Aoi's rumour soon comes out.

Souta spends the day looking after the little girl who came before, leading Popura to start feeling a little left out. The next day, Aoi comes across Haruna, seeing her as a potential mother and bringing her to Wagnaria, where the other staff try to keep her put until Otoo returns, but she somehow manages to escape regardless.

As Sōta feels conflicted over his feelings towards Mahiru, Aoi, wanting Hiroomi to give her some attention, tries to obtain information on the blossoming relationships. Later, Popura gets a toothache and takes the day off, having a dream where she becomes a magical girl. Meanwhile, Kirio ends up discovering Aoi, who is revealed to be the sister he was searching for, and is met with resistance when he tries to take her back home.

Staying over at Sōta's house, Aoi explains her backstory about being constantly forced to study by her mother, inevitably pointing out the reason she ran away was because Kirio ate her natto. As the other staff members try to convince Aoi to return home over the next few days, Popura asks Kirio to bring over his mother, Kikuno, who is revealed to have trouble talking with others clearly to the point that her children need a manual to understand her.

With Aoi's situation resolved, Sōta continues to be in denial over his feelings for Mahiru. Meanwhile, having finally learned Yachiyo's birthday, Jun gives her all the presents that he hadn't had the courage to give her before. Later, Aoi gets herself a cellphone, which she attempts to use to communicate with Kikuno, while Popura becomes depressed when she believes she's gotten shorter.

As Popura becomes more aware of the relationships blooming around her, she and Aoi question Otoo about the restaurant's stance on romantic relationships. Later, Minegishi comes to the restaurant to tell Sōta something and gets punched by Mahiru, leading her to feel she hasn't gotten over her androphobia, but Sōta manages to calm her down.

Jun finally works up the courage to confess to Yachiyo, but it doesn't go well and Yachiyo goes into hiding. After managing to find her, Jun gives a direct confession which she finally reciprocates. Afterwards, Kyoko seems to want to stop Yachiyo making parfaits for her, saying she shouldn't be tied down to her, but Jun accepts that Kyoko is a key part of the girl he fell in love with.

Aoi, curious about Sōta's delayed reactions, is tasked by Yachiyo with taking a photo of Hiroomi for an album. Meanwhile, as Sōta and Mahiru go on their date, they are interrupted by Mahiru's father, who Mahiru hits when he starts insulting Sōta, managing to work things out with him. Later, Yachiyo announces her resignation to the rest of the staff, with Sōta encouraging Popura to do her best as the next chief before being mysteriously abducted.

As Sōta stops showing up at work, Kyoko learns that he has been spending a lot more time crossdressing because of his mother. Worried she is the cause of her problem, Mahiru confronts Sōta and tells him how she thinks of her, but Shizuka catches him and forces him to quit working at Wagnaria. Learning from Kyoko that Shizuka is having Sōta crossdress until he learns to be honest about his feelings, Mahiru heads off to talk with Shizuka, having to confront each of the Takanashi sisters along the way. As Mahiru confronts Shizuka with help from Nazuna, Popura shows up and convinces Shizuka to let Sōta keep working. Afterwards, Shizuka returns to her work while Sōta and Mahiru finally confess to each other.