Note: for the joke article, see episode 12.
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 where we left off the last episode –Makoto and Kotonoha are still outside, walking the streets with Kotonoha cling on to his arm. Makoto stops and mutters to himself it is cold … then Kotonoha takes his hands and places them on her chest. Overall she still looks out of it, despite her eyes no longer being in a complete yandere state.

Meanwhile Sekai is at Makoto’s apartment, cooking dinner while looking rather depressed and looking at a picture in her cell phone of her and Makoto dancing by the bonfire. She decides to call Makoto because she wants to have dinner with him, but he refuses. Sure enough – he is in a restaurant, having dinner with Kotonoha. The argument gets rather heated (involving Sekai’s pregnancy) and in the end Makoto yells at her to go home and hangs up. Then the sound of plates crashing is heard.

Sekai leaves his home in a fit of rage, while Makoto and Kotonoha get on a train to Makoto’s home. Sekai, requires a train ride home, but, as she was walking towards the station, she sees a passing train that catchers her eye instantly. Inside Makoto and Konotoha are on the train together, with Konotoha holding onto Makoto's are, much to her disbelief and horror. As such, she turns back and the way she came from.

Makoto arrives home with Kotonoha and he goes to make some tea. In the kitchen, he finds a array of food and cookware sprawled on the ground, obviously done by Sekai, before leaving the house. Makoto starts to clean the mess up, though he isn’t angry. The doorbell rings and Makoto goes to answer. As Makoto heads to the doorway to answer, Kotonoha is already there. When she opens the door Sekai slaps her across the face. Sekai starts accusing Kotonoha of being here and demands that she leaves while she continiously shakes the living day lights out of her.

Kotonoha reacts calmly though and in turns says it is Sekai who is trying to pull Makoto and her apart. Also, mentioning that Setsuna must have been acting on Sekai’s behalf as well. Sekai doesn’t understand and Kotonoha reveals Setsuna loved Makoto as well, which is a huge shock for Sekai. Then Kotonoha says she won’t hesitate anymore and kisses Makoto. The kiss becomes more heated and Sekai leaves, confused and very, very upset.

As she is walking home Sekai remembers a conversation with Setsuna from a while back. when she had told her about Makoto. The scene shifts to darkness and several cloaked figures with masks are present. The person with red mask accuses Sekai of being the one actually responsible for all this. When Sekai tries to deny it, the figure removes the mask, turning out to be Setsuna, which causes Sekai to break down.

Next morning Sekai gets a message from Makoto and is overjoyed. As expected, her joy is short lived, as Makoto mentions one of Kotonoha’s acquaintances in a hospital, basically saying she needs to have an abortion.

In school Makoto looks relieved that Sekai has not come. He is happy he gets to spend one on one time with Kotonoha. They eat lunch on the school roof and Makoto acts lovingly towards her. The two share a fairly romantic kiss.

Evening brings Makoto a not so pleasant experience – a conversation with Sekai. He asks her how did it go, but she does not answer. After a moment of silence Makoto gets up to get the tea, but Sekai abruptly gets up and goes instead. While in the kitchen she takes out her cell and sends a message to Makoto, which distracts him. While he goes to get his cell she glares at him while holding a knife in hand.

Makoto checks the message and is surprised to see it is from Sekai. First line reads “I am sorry”, followed by a lot 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 gut and falls to the ground. Sekai yells he is horrible and continues to repeatedly stab Makoto who is incapable of resisting. Makoto ends up dying from all the blows. Horrified at what she has just did, Sekai leaves the house in a absolute hurry.

Sometime later, Sekai gets a message from "Makoto". Sekai, then goes to the rooftop. To Sekai's surprise, it is not Makoto but, Kotonoha, who is carrying a bag with her. They have an argument and Kotonoha does not believe Sekai was actually pregnant. Then Kotonoha says, "Makoto is right here" and points Sekai towards the bag she has brought along. Sekai reluctantly open it and instantly drops to her knees, vomiting. The decapitated head ok Mokoto is discovered in the bag, indicating that Kotonoha, cute off his head to bring it along with her. Kotonoha then reveals to be holding a cleaver (or japanese saw). She wonders if that is really so (about the pregnancy) and says she will investigate for herself and dashs forward. Sekai pulls her knife out (still withholding Mokoto's blood), but Kotonoha disarms her and slices her neck, killing Sekai. After that she slices Sekai’s stomach open and comments in a bored voice, "she was not pregnant after all". Later we see Kotonoha lying on a yacht, drifting in the sea, while cuddling with Makoto’s head, muttering how they are alone at last and will be together forever.

Then the credits begin to roll. In a post-credits stinger, we see that everything in school becomes back to normal (we also see Taisuke with an unseen character that somewhat resembles Makoto) and we hear Makoto's dialogue from when he was just looking at Kotonoha from afar. The scene shifts and ends with Makoto's cellphone on the bench where he, Sekai and Kotonoha used to sit together to eat lunch.