JB drops Yūji off at the Academy after a job but before he can exit the car she kisses him on the cheek, much to his discomfort. To complicate matters, he finds that Sachi has witnessed the kiss but promises not to say anything. Yūji returns to his room to find Amane waiting for him. Following their usual banter and a shower, Yūji sits down to dinner when Amane receives a picture of JB kissing him (Sachi took 'saying' literally), which arouses her jealousy. Yūji asks Amane why she is so persistent in pursuing him to which she responds it was love at first sight. He is not satisfied with her answer and presses her. She breaks down and to Yūji's shock mentions his sister's name. She reveals that she and Yūji's sister, Kazuki, were both freshmen on the same basketball team in middle school. As they talk further Yūji finally agrees to allow her to act as his girlfriend provided that he does not have to act as her boyfriend. Amane then retrieves a journal from her room and gives it to Yūji to read. The journal documents the tragic events that befell the basketball team as Amane, the sole survivor, remembers them.

The survivors of the crash continue to make do as Kazuki continues to care for the wounded. As the days pass, they bury their dead and continue to gather what little food they can find. Their teacher, having scouted around, takes half of the food and leaves, promising that he will return with help. Despair sets in when he does not return after a couple of days. Malnourished, some of the girls start acting strangely. Finally, the pet dog of one of the girls perishes and is butchered to provide the survivors with sustenance.

Two weeks pass and no rescue is in sight and the injured and malnourished girls start dying one by one. When their teacher returns without help, all remaining hope is lost. When sensei claims to have hunted down a deer, Kazuki is suspicious and decides to set out with Amane in tow. She shows Amane that the 'venison' that the others ate was in fact something else and that the remaining survivors have gone mad and are active participants or do not care. When the others close in on the fleeing pair, Kazuki stays behind as a decoy to let Amane escape. At first hailed as a miracle survivor, Amane soon faces questions as to why she was the only one who survived. Suffering from nightmares, the relentless public pressure convinces her that she must be punished for living when everyone else died and that Yūji is the person with the greatest right to punish her. She even asks Yūji to kill her. Yūji instead asks her to live for his sake as her punishment in the hope that since he has accepted her, even knowing her past, she will come to forgive herself.

Yūji accompanies Amane to the site of the accident so that she can finally put the incident to rest. On the way, Yūji is stopped by a man who claims to be Amane's greatest fan. After she pays her respects to her dead friends, Amane leads Yūji to a location on the map that Kazuki gave her where they find a note hinting that Kazuki is still alive. Meanwhile, the man who accosted Yūji has entered the Academy and taken the other girls hostage and demands Amane's presence. When they return home, Amane prepares to give herself up and Yūji, having been able to listen to the goings-on in the school via cell phone, comes up with a plan to end the standoff. The hostage taker is revealed to be the father of Chiaki Sakashita who has not been able to deal with the death of his daughter and wants to kill Amane for surviving. Having decided that shooting Amane would be too easy a death, Sakashita removes her to the washroom to have his way with her. Yūji is able to snipe Sakashita through a 10 cm wide field of view from over 900 m away, ending the hostage situation and reuniting him with the girls. Following a time skip of one year, an unidentified boat enters Japanese waters. One of two passengers fires a rocket at the Coast Guard cutter and helicopter. The other opens a music box.

Yuuji makes the unexpected decision to pursue promotion within the institution he works for. He meets with JB to discuss the documents he submitted for review as a part of the promotion process, documents pertaining to his own past.

After Yumiko gets in touch with the informant "Jimmy," she and the other girls at Mihama Academy learn that the current situation is even worse than they thought. Although they have lost Yuuji and have been driven from the academy, they secure a new base of operations and plan a rescue mission for him.

Yuuji and his sister play doctor.

Special bonus video included with the "Le Fruit de la Grisaia Vol.6 [Limited Edition]" set on Blu-ray and DVD.

A formless supporter, "Thanatos," suddenly supports Amane and the others. "Her" objective is also to liberate and rescue Yuuji Kazami. Thanatos and the Mihama girls' interests align and begin preparing to execute their mission. The girls are perplexed by Thanatos's seemingly cryptic instructions that unfold via cell phone, but they bring the girls better results than they ever expected in bringing their goal to fruition.

The international terrorist Heath Oslo uses nuclear weapons as a shield to threaten the nation. The nation plans to make Yuuji a human sacrifice in their dealings with Oslo. There is no other way to save Yuuji from this crisis but to rescue him as he is transferred from Ichigaya to Akasaka.

The Mihama girls have executed their intense getaway and have rescued Yuuji. Waiting at their goal is Kazuki Kazami, who lived as the core of Thanatos for a long time. This unexpected encounter leaves Yuuji and Amane unable to hide their surprise, but circumstances don't allow them time to savor their emotional reunion.

Tartarus, a gigantic, man-made island, floats on the Pacific Ocean. It is both the adversary of society, and the castle of Heath Oslo, Yuuji Kazami's mortal enemy. Oslo quietly awaits the moment Yuuji Kazami, the final key he needs to fulfill his ambitions, appears before him once more.

Short released with the fifth volume.