Well, a storyline might involve Usui and Misaki facing some challenges during the pregnancy. It could be that Misaki has a difficult pregnancy and Usui has to be extra supportive. He might take on more chores and help her with her daily tasks. Or perhaps they have to deal with financial concerns. They start thinking about how to afford all the baby stuff like diapers, strollers, and cribs. They could also be thinking about their future and how the baby will change their relationship in the long - term.
A possible story could start with Misaki finding out she's pregnant. She's initially scared and not sure how to tell Usui. When she does, Usui is overjoyed but also a bit worried. They then go through the process of telling their parents. Misaki's parents might be a bit strict at first but then come around. As the pregnancy progresses, they start taking parenting classes together. Usui might also start reading books on pregnancy and parenting to be more involved. Along the way, they have cute moments like feeling the baby kick for the first time and arguing over baby names.
One possible storyline could be about how Usui and Misaki deal with the upcoming baby in the midst of their studies or work. For example, they might have to balance school exams and doctor's appointments. Another could be the reactions of their friends and family. Maybe Misaki's friends are super excited and start planning a baby shower right away. And finally, there could be a storyline about the couple preparing their home for the new arrival, like painting the nursery.