Every day, Naoto Hachiouji is teased relentlessly by Hayase Nagatoro, a first year student he meets one day in the library while working on his manga. After reading his story and seeing his awkward demeanor, she decides from that moment on to toy with him, even calling him Senpai in lieu of using his real name. At first, Nagatoro's relentless antics are more bothersome than anything and leave him feeling embarrassed, as he is forced to cater to her whims. However, as they spend more time together, a strange sort of friendship develops between them, and Naoto finds that life with Nagatoro can even be fun. But one thing's for sure: his days will never be dull again.

Tooru Honda has always been fascinated by the story of the Chinese zodiac that her beloved mother told her as a child. However, a sudden family tragedy changes her life, and subsequent circumstances leave her all alone. Tooru is now forced to live in a tent, but little does she know that her temporary home resides on the private property of the esteemed Souma family. Stumbling upon their home one day, she encounters Shigure, an older Souma cousin, and Yuki, the prince of her school. Tooru explains that she lives nearby, but the Soumas eventually discover her well-kept secret of being homeless when they see her walking back to her tent one night. Things start to look up for Tooru as they kindly offer to take her in after hearing about her situation. But soon after, she is caught up in a fight between Yuki and his hot-tempered cousin, Kyou. While trying to stop them, she learns that the Souma family has a well-kept secret of their own: whenever they are hugged by a member of the opposite sex, they transform into the animals of the Chinese zodiac. With this new revelation, Tooru will find that living with the Soumas is an unexpected adventure filled with laughter and romance.

High school student Makoto Itou first notices Kotonoha Katsura at the start of his second semester, freshman year. Immediately, he becomes entranced by her beauty, but his bashfulness doesn't allow him to approach her, even though they ride the same train every day. Instead, he snaps a photo of her in secret and sets it as his cell phone's wallpaper: a charm that, if kept under wraps, would supposedly help you realize your love. However, classmate Sekai Saionji spots the picture, but instead of ratting him out, she offers to help set him up with Kotonoha—going so far as befriending her just for him. Thus, the trio begins a rather impromptu friendship. School Days follows the lives of these three teenagers as they traverse the joys and hardships that come with being a high schooler. In a story alive and brimming with romance and melancholy, the tale of these three students will linger in memory long after the momentous conclusion.

Spirits are otherworldly entities with immense power, capable of creating spatial quakes whenever they appear. One way of dealing with them is through brute force and killing them... or making them fall in love and sealing their powers. Having sealed three Spirits, Shidou Itsuka continues his mission with Ratatoskr in locating more spirits and dating them, to ensure the world's safety from further destruction. However, this time around, their problems will not be limited to Spirits as a more imposing threat seems to have noticed their activities.