The story is about a love triangle between the male protagonist Makoto, and the two heroines Kotonoha and Sekai. Makoto develops a love interest in Kotonoha, a girl in the same year but different class. Although they both take the same train to school, she is unaware of his existence. His classmate, Sekai, manages to put the two together despite holding strong feelings towards Makoto.

During the freshmen orientation, Makoto Itou met Kotonoha Katsura and immediately developed a crush on her. They would ride on the same train together every morning, and all Makoto could do was make himself look busy by looking at the standby screen on his cell phone...

Makoto and Kotonoha go on their first date together, and Makoto's heart and mind are in a whirlwind of excitement and bewilderment, but it doesn't go as he had imagined it to go. The next day, Makoto later tells Sekai about the date, and she tells him to slow it down and not smother her. She gives him two movie tickets to take Kotonoha on another date...

When Kotonoha first started dating Makoto, they did not mesh well together. Makoto's thoughts were all over the place thinking about Kotonoha. He saw Kotonoha in the train in a bad mood and tried to hug her but she refused. Hikaru, who is in the same class as Makoto, happened to see this.

Makoto wants to develop his way of expressing himself. He was on the school's rooftop with Kotonoha when he tried to get close to her, but didn't expect for her to turn him away. As that things didn't go so smoothly, Sekai turns to Makoto, and makes a proposition...

Makoto and Kotonoha go to the pool for a date on the same day as Sekai and 6 of her friends. At the pool, it's clear that Makoto and Kotonoha are dating, however it seems as if Makoto has developed feelings for Sekai, hinting her that he wants to be with her instead. Sekai keeps reminding him that he's Kotonoha's boyfriend and cannot be with her, and tells him to forget about the "practice".

Things have developed with Sekai and Makoto. From the outside, it seems like Makoto is still involved with Kotonoha, however his relationship with Sekai has accelerated. While, Sekai knows its bad to keep lying like this, she can't turn away Makoto. Gradually, Makoto starts avoiding Kotonoha by not answering if phone...

Makoto has put out the outwardly appearance that he is avoiding Kotonoha, as his relationship with Sekai has developed even more. Setsuna has noticed that their relationship together has changed, and tells Makoto to stay away from Kotonoha and cut off all communication with her, for Sekai's sake. But the web of lies and relationships starts to get tangled...

Makoto hasn't told Kotonoha yet of his relationship with Sekai. However, one night Kotonoha bumps into Sekai outside of Makoto's apartment and an altercation goes down. And with that, begins the the school festival...

Makoto makes a promise to Sekai to dance with her during the School Festival's folkdance; however, he also made the same promise to Kotonoha. As Kotonoha mans the front desk at her class' school festival activity, she ferverously texts Makoto and awaits for a single response back...

As the school festival comes to an end and Makoto and Sekai dance at the bonfire, it finally seems like they're happy together and things have settled down. However, Kotonoha watches from the shadows, and obstiantly denies what has happened still believing that their still going out. Meanwhile, as Setsuna prepares to move to France she is doing some final preparations to ensure that her best friend - Sekai - will be taken care of...

Christmas is coming around the corner, and although Makoto is dating Sekai, it seems as if he wants out of it. So it appears as if he is haphazardly getting himself involved in other relationships, despite his promise to Setsuna. Now things are going terribly wrong, as Kotonoha loses herself, Sekai finds out about Makoto's infidelity, Setsuna's move to France and most importantly a sudden change to her body...

Sekai disappears, and Makoto is wandering around aimlessly until he meets up with Kotonoha again, under the town's Christmas tree. As they pass the night together and Sekai witnesses the two of them heading back to Makoto's place. Just to make sure her eyes weren't playing tricks on her, Sekai heads over to his place...

OVA coming with the PlayStation 2 game "School Days L×H" It's a very funny comic spin on Valentine's Day, and much more lighthearted than the original series.

Originally an April's Fool in 2007, this one episode OVA is a spin-off of the School Days game by 0verflow, and shows Kokoro Katsura, the little sister of one of the main characters, from her other side. A mahou shoujo out to save the world, or something like that.