The common route in Grisaia no Kajitsu consists of various slices of life of Yuuji’s time within Mihama Academy. Mihama Academy, funded mainly by the Sakaki family, is a rather special school, housing only six students, each with their own set of special circumstances. It serves mainly as an introduction for each of the characters by revealing each of their personalities and quirks, as well as showing a few aspects that they try to keep hidden. Each of the characters accept Yuuji’s entrance to the school with varying levels of acceptance, but over time they all grow closer to him through the myriad of events they experience together.

After having Yumiko chase him around with a box cutter, warding off Amane’s constant advances, dealing with Michiru’s stupidity, being awed by Sachi’s competence, introducing Makina to a variety of new things, and teasing JB and Chizuru, Yuuji is faced with several choices.

The first with regard to Makina, from whom he receives a cryptic text message. The message in question tells Yuuji that he’s been promoted, from “onii-chan” to “papa”. Unsure of what this is supposed to mean, Yuuji decides to talk to Makina in person, where she offers to buy Yuuji’s services in exchange for her entire funds: 70 million yen. Surprised by the amount of money that Makina has, Yuuji is faced with a decision. To accept or reject her offer? Accepting Makina’s offer to become her “Papa” will set Yuuji onto the Makina route, while declining the offer will lead Yuuji to his next choice.

The second major choice Yuuji has to make is about how he should deal with Amane’s forward behaviour. After spending a day at “work”, Yuuji returns to his room to find Amane faithfully waiting for him. Just how far do Amane’s affections for him go? Since Amane seems to be underestimating men, does he go for shock and awe, stealing a kiss with overbearing force? Or does Yuuji simply ignore Amane’s idiocy, since getting caught up in her nonsense would be giving her exactly what she wants? Choosing to kiss Amane will put Yuuji onto Amane’s route, while ignoring her will lead to Yuuji’s next choice.

The third major choice for Yuuji occurs as he enjoys his everyday life in Mihama Academy. He finds Makina and Sachi playing a strange word game. After Makina gets tired of it, Yuuji decides to try going against Sachi in the game, with the loser having to carry out a penalty for the victor. After a while of playing the game, Yuuji makes a mistake and loses, leaving Sachi with a single demand for Yuuji: Praise her for having defeated him. Unsure of why Sachi would ask for such a bizarrely simple penalty, Yuuji asks Sachi why she would request that, though Sachi herself seems rather unsure so as to why. And so Yuuji is left to decide whether he wishes to give Sachi the praise that she desires, or to ask for an alternative penalty. Praising Sachi will cause Yuuji to travel down Sachi’s route, while asking for an alternate penalty will leave Yuuji with his final choice.

With classes over for the day, Yuuji finds Amane, Makina, and Sachi discussing the topic of friendship. To be specific, whether or not a true friendship between a man and a woman is possible. With not much knowledge about friendship in general, Yuuji tries to avoid joining the conversation. Yumiko passes by without contributing anything before Michiru excitedly makes her appearance. However, when Michiru finds out that the discussion was about friendship, her mood plummets and she quickly finds an opportunity to leave. Yuuji decides to follow after Michiru and finds her outside the school in a foul mood and having chest pains. When Yuuji tries to ask Michiru what’s happening, she responds angrily that he should leave her alone and exits the school grounds.

Yuuji decides to go looking for Michiru again and finds her on that high ridge overlooking the sea. However, the Michiru Yuuji finds isn’t the Michiru he knows. The other Michiru is rather impressed that Yuuji could tell the difference, since nobody else had noticed her until this point, and changes her demeanor completely. The two hold a surprisingly complex conversation until the Yuuji decides that they’ve talked for long enough. Realizing that this girl had just forced a retreat from him, Yuuji can choose to either enquire further about her or ignore her. Choosing to enquire further about the girl will put him onto Michiru’s route and result in Yuuji and the other Michiru kissing, before the original Michiru reappears without a clue so as to why she or Yuuji are on the ridge while choosing to ignore her will put Yuuji onto Yumiko's route and result in the first scene of her route; Raison d’Etre.