Yuri and Otonashi watch over an unconscious Kanade at the Nurse's Office. Yuri blames herself for what happened to her. Otonashi, however, tells her that she should not make herself responsible, as her action ended up saving the SSS from a worse-case scenario involving Kanade's Harmonics clones.
The leader of the SSS leaves, and it is there that Otonashi expresses his helplessness to Kanade's condition.
Meanwhile, the remaining members discuss about Kanade in the SSS's headquarters.
They realize that they have seen Kanade in this condition for the first time. Yuri is optimistic that Kanade will wake up at any moment, but Shiina points out that they have no idea which Kanade would they see awake. The others want to be optimistic that Kanade will turn out back to her usual self when she wakes, but they also know that all those consciousnesses she absorbed will have a tendency to manifest as well. Yuri points out that if there are 100 clones, then she has about 1% chance of returning to normal.
DAY 1.Otonashi finds himself lying down. He checks the time and he realizes that he missed the entrance exam. As he stands up and looks around, it is there that he realizes the gravity of his situation.
Everything is dark. Some of the passengers with him are covered with blood and are motionless, while others are trying to help each other.
He sees an injured person behind him and tends to his aid. Otonashi then carries him out of the train and soon, they saw the extent of the damage received by the train. Otonashi tries to contact help using his phone, but being inside a tunnel, the signal is too weak for him to call anyone. With that, he decides to help out instead. With the help of the injured man, named Igarashi, they venture out inside the mangled wreckage.
Soon, they found more and more survivors, some lucky to have only cuts and bruises, while some require first aid. With Otonashi's medical knowledge, he and Igarashi proceed to rescue the survivors.
After a few hours of search and rescue, Otonashi decides to head out to look for an exit.
However, he discovers that the other end of the tunnel is also blocked by rubble. What's worse is that he can't contact from his phone still, and he discovers that he also receives injuries from the accident (bruised stomach, few cuts). Otonashi returns and honestly breaks the news to anyone. He also tells that they would need everyone's help to survive. Despite there are some who question his authority that time, Igarashi tells everyone that he has medical knowledge. Otonashi then reassures everyone that everything will be fine.
DAY 2.With the water Igarashi has in his luggage, they rest and wait for the rescue teams to arrive. Igarashi and Otonashi assists everyone to their needs. While disscussing the food storage, Igarashi praises Otonashi's ability to help out in such a situation.
Suddenly, one of the survivors attempt to hoard the water supply. He is almost immediately apprehended by two other survivors, but the water he tried to steal ends up wasted. The other passengers complain about that he just did, but Otonashi tells them that what was wasted will be his share. Igarashi decides to give part of his share to Otonashi.
Otonashi wakes up to a dire news: one of the survivors have passed away in his sleep; his eyes are still with a bit of what appears to be vomit in the side of his face. He tries to resuscitate him, but it was no use. He falls into lethargy, thinking about failing to do what he must and ending up losing a life because of it.
DAY 7.Otonashi, for a moment, remembers one of his visits to his sister Hatsune. He also remembers her mentioning the need for a donor,
He later borrows a ballpoint pen from Igarashi. At that time, he pulls out a card and reads about its contents, which includes a consent for the bearer of that card to donate one's organs when they become brain dead. Upon following the instructions, he circles all of the options and signs his name on it. Igarashi follows suit, and soon, everyone does the same thing.
Igarashi tells again Otonashi how he is a great person. At that time, drills are heard and light shines on Otonashi's face, as he dies peacefully.
Igarashi continues to call his name as everyone is saved.
Soon, Otonashi wakes up with the feel of Kanade's hand on his head. He blurts out how worried he was, and Kanade, in return, was relieved that he has awakened. He recollects on what happened to him in his last moments and on his relief that he has saved someone through his body.
He realizes that he would disappear if he would not have any regrets in life. Kanade, however replies that he can stay if he wants to make everyone happy.
Otonashi soon realizes that Kanade has a unique way of doing things and thus, holds a huge misunderstanding with the SSS.
Also, Kanade wants everyone to experience a fulfilling youth, and the "afterlife school" is there to teach them that. And that same principle clashed with the ideals of others, resulting in a clash that spanned countless days between them and Kanade.
Soon, Otonashi offers to be friends with Kanade, and now, being the person befriending the opposite sides of the battle against God, he decides to do something: to make everyone graduate in the afterlife school.
Meanwhile, the NPC students are gathered in the auditorium and it is there that the faculty announces Kanade's innocence with regards to the incident which led to her dismissal from being Student Council President. Her position is reinstated, and Naoi is given a new title: Deputy Student Council President.
On the other hand, Yuri and the others suffer the punishment for the ploy which caused Kanade's dismissal; a retake of the exams. As the others fight in the middle of the examination, Otonashi thinks over his plan to cooperate with Kanade, who has miraculously lost his memories of the last few days. That plan involves making Kanade Student Council President once again and moving according to his plans as SSS's usual enemy.
Otonashi finally becomes the one who would put everything to place.
But even he is curious as to what would happen after all of this.
- Igarashi - one of the survivors of the train crash where Otonashi is also involved. Being the first person to be saved by Otonashi, he helps him out to save the other survivors and becomes his companion throughout the seven-day ordeal which ended with Otonashi dying.