Warning Contains spoilers for the events of episode 12 (season finale) of School Days. Avoid reading if you have not yet seen this episode.

Episode 12 is the final episode of School Days, in the anime adaptation.

The finale to the anime starts off picking up where we left off the last episode. Makoto and Kotonoha are still walking the streets, with Kotonoha clinging on to Makoto's arm. Makoto stops and mutters to himself it is cold before Kotonoha takes his hands and places them on her chest.

Meanwhile, Sekai is at Makoto’s apartment, having cooked dinner and looking rather depressed, staring at her cellphone background, which is Setsuna's picture of her and Makoto dancing by the bonfire. She calls Makoto because she wants to have dinner with him, but he refuses, as he is already dining with Kotonoha at a fancy restaurant. The argument becomes rather heated (involving Sekai’s pregnancy) and ends with Makoto yelling at her to go home before he hangs up. Then, the sound of plates crashing is heard.

Sekai leaves his apartment in a fit of rage, while Makoto and Kotonoha get on a train to Makoto’s home. Sekai rides a train home, but as she is about to leave the station, she sees Makoto and Konotoha together on a passing train, much to her disbelief. As such, she turns back the way she came from.

Makoto arrives home with Kotonoha and goes to make some tea. In the kitchen, he finds an array of food and cookware sprawled on the floor, a "parting shot" courtesy of Sekai. Makoto starts to clean the mess up, though he is more contemplative than angry. The doorbell rings and Makoto goes to answer, only for Kotonoha to have answered the door only to get slapped by an irate Sekai. Sekai starts accusing Kotonoha of seducing Makoto and demands that she leave.

Kotonoha reacts calmly, however, and in turn accuses Sekai of trying to pull Makoto and her apart, even colluding with Setsuna. Sekai doesn’t understand and Kotonoha reveals that Setsuna loved Makoto as well, which is a huge shock for Sekai. Kotonoha then claims that she won’t hesitate anymore and kisses Makoto. The kissing becomes more heated and Sekai leaves, devastated.

On her way to the train station, Sekai remembers a conversation with Setsuna from when she first told her about Makoto. The scene shifts to darkness and several cloaked figures with masks are present. The red-masked figure accuses Sekai of being the one to set all this in motion. When Sekai tries to deny it, the figure removes the mask, revealing herself to be Setsuna, which causes Sekai to break down.

That night, Sekai gets a text from Makoto and is overjoyed. However, her joy is short-lived, as Makoto mentions one of Kotonoha’s acquaintances in a hospital, implying that he wants Sekai to get an abortion.

At school, Makoto is relieved that Sekai is once again absent. However, he receives a text from her asking to meet her at his apartment after school. He and Kotonoha eat lunch on the school roof and Makoto acts lovingly towards her. The two then share a fairly romantic kiss.

That evening, Makoto asks Sekai how it went at the hospital, but she does not answer. After a moment of silence, Makoto offers to make some tea, but Sekai abruptly gets up and goes to do so herself. While in the kitchen, she sees the food that she'd made the night before in a garbage bag. After this final straw, she takes out her cellphone and sends a text to Makoto, which distracts him. While he goes to answer it, she stares after him while holding a kitchen knife.

Makoto checks the message and is surprised to see that it's from Sekai. The subject reads, “I'm sorry”, followed by a series of empty spaces. When he finally gets to the last one, it reads “goodbye”. Makoto turns around with a shocked expression, only to find Sekai charging at him. Before he can react, he is stabbed in the stomach and falls to the ground. Sekai shouts that he is cruel for wanting to be with Kotonoha and continues to stab Makoto, who ends up dying, groaning Sekai's name. Horrified at what she has just done, Sekai leaves the house in a panic.

That evening, Sekai gets a message from "Makoto", inviting her to meet "him" at the rooftop. To Sekai's surprise, it's not Makoto, but Kotonoha, who has been waiting for her. They then have an argument, Kotonoha revealing that she doesn't believe that Sekai was actually pregnant. When Sekai insists that she is, Kotonoha points her to the duffel bag she has brought. Sekai reluctantly opens it, then drops to her knees after looking inside, vomiting. Kotonoha then takes out her dozuki (or Japanese saw), before dashing forward, claiming to want to verify Sekai's pregnancy. Sekai pulls her own knife out (still stained with Makoto's blood), but Kotonoha disarms her and slices her neck, killing her. She slices Sekai’s stomach open and comments, "There's nobody inside". Later, we see Kotonoha lying on a yacht, drifting in the sea, while cuddling Makoto’s head to her chest, happy that they are alone at last.

In a post-credits stinger, we see that everything in school becomes back to normal. There are also cameos of Otome's younger sister Karen and Nijou twins Kazuha and Futaba. Taisuke is also seen with an unseen character who somewhat resembles Makoto. We hear Makoto's dialogue from when he was simply admiring Kotonoha from afar. The scene shifts and ends with Makoto's cellphone on the bench where he, Sekai, and Kotonoha used to eat lunch together .