A young man walks a distance of 175 km and moves to Mishima Cape with a single backpack on him: Yuuji Kazami. The wish of this man so free from worldliness was thus: "I want to enter an ordinary school and lead the life of an ordinary student."

Yumiko Sakaki attempted to cut Yūji with a blade but fails each time in doing that. He somehow got along with Makina, who is actually quite shy, after he helped her to catch the crayfish. He then visits the principle's office for advice on resolving Sakaki's hostility towards him. He also found out that all of the students, including him, have special circumstances that are sensitive. Yūji's guardian and work boss, JB comes to pay him a visit outside of school. This caused his classmates to question him of JB's identity, especially Amane who is concerned whether Yūji has a girlfriend or not. Later, in the evening, he was ambushed by Yumiko with a blade and he responded by grabbing the hand which is holding the blade. He then tell her that he is not her enemy and intended to be her friend. From that day onwards, Yumiko is no longer hostile towards him and treats him as another student in the academy.

Michiru tries to run away from reality after losing Meowmel and does something impulsive. Yuuji finds her quickly, and she survives without issue thanks to him. The next day, Michiru acts as cheerful as can be, like what happened the day before was all a lie. She's the same tsundere and idiot as always...

Michiaki Sakaki, Mihama Academy's chairman, makes use of his influence and summons JB to his side. He becomes fed up that the academy he specifically created to put Yumiko, who is supposed to succeed the Sakaki home's headship, in line isn't fulfilling its purpose. He decides to borrow the strength of JB's "company" to do so.

Yuuji suddenly announces that he'll be Makina's father. Everyone around gets confused and looks at them skeptically, but the two of them act like father and daughter very dilligently. Yuuji even becomes a rather Spartan father at the end of the term. He attempts to drive all the knowledge he possesses into Makina, from hand-to-hand combat techniques to marksmanship.

Yūji takes the job JB gave him but only so that he can protect her. To do so, he and Makina leave the Academy so as to present a moving target and Sachi gives Makina an apple sapling as a parting gift. The efforts of the organization to get hold of Makina are fruitless as Yūji is able to dispose of every agent sent after them. As they flee, Yūji becomes aware of Makina's recurrent nightmares involving her father. It is revealed that a few years earlier Makina's father found evidence of the Irisu Group's corruption and was killed in front of Makina on his wife's orders. Makina spent a number of years in a hospital recovering from the trauma. It is further revealed that she has a near photographic memory and had read some of the incriminating documents before her father's death. It turns out that Makina's mother ordered the hit on Makina because she phoned her mother and threatened to reveal the corruption unless her younger sister was kept safe.

When their latest hideout is compromised, Yūji manages to get them away but Makina forgets her sapling. Despite Yūji's admonition to forget about it, Makina returns to the hotel to search for it and is shot. Yūji shows up in time to take her to a hospital but is intercepted by JB. In the hospital, Makina's mother shows up and, to JB's horror and disgust, asks if Makina's internal organs are unharmed because Sarina is in need of an organ transplant. Later, a disguised Yūji shows up at the Irisu Group's HQ and shoots Makina's mother. With the contractor for the hit out of the picture, and with hard evidence of the Irisu Group's corruption in the hands of the organization, Yūji and a recovering Makina return to the Academy.

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.

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.

Asako Kusakabe rescues a young Yuuji from terrorists on a certain mission. She has evaded death as a soldier time and time again, and on a whim decides to become Yuuji's guardian. Although she partially forces it, and despite her coworker JB's concerns, the awkward female soldier and young man begin to live under the same roof.

Asako's poor health begins to interfere with her work. Yuuji senses her change in condition, and as he covers for her, he starts to think he may have found his life's meaning. Asako tries to respect Yuuji's resolve, but JB, who watches over both of them closely, is apprehensive about Yuuji's attempts to return to that violent world.

Yuuji moves forward on his path as a soldier to protect "an important woman": Asako. However, she leaves his side without waiting until he's reached maturity. Yuuji is yet again tormented by a sense of helplessness, but is saved by Asako's parting words and begins to be able to walk on his own two feet once more.

After Yuuji suddenly disappears, the girls at Mihama Academy notice him on the TV screen. What's more, it's being reported nationwide that he's a suspect in a terrorist plot which will likely turn into an international incident.

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.

Special bonus video included with "The Labyrinth of Grisaia: The Cocoon of Caprice 0" Blu-ray and DVD release.

Short released with the first volume.

Short released with the second volume.

Short released with the third volume.