In a sea of amazing young men, Keita struggles to find out what makes him unique, and how he can possibly deserve to be treated as an equal by the students of Bell Liberty.

In the original game, the player Keita Itō suddenly received an acceptance letter from the renowned Bell Liberty Academy (also known as BL Gakuen).

However, on the day of his transfer, the bridge joining the school and the academy, which was located on a remote man-made island, suddenly raised and his bus fell.

Luckily, no one was injured but the accident aroused the attention of both the student council's president Niwa Tetsuya as well as the head of the accounting department Saiyonji Kaoru.

In the sequel Gakuen Heaven 2 ~Double Scramble!~ (学園ヘヴン２ ～DOUBLE SCRAMBLE！～), released in April 2015, the player Yuki Asahina is invited to study at the near-legendary Bell Liberty Academy despite possessing no remarkable skill or a talent of any distinction save his uncanny good luck.

There is little for Yuki to celebrate, however, as the position of student council president has been reduced to a powerless servant, responsible for nothing besides the menial chores that Durak, Bell Liberty's disciplinary committee and the school's true authority, consider beneath them.

After befriending classmate Tomo Kasahara and student council peers Kuya Sagimori and Masatsugu Takato, Yuki is introduced to the other important students in the game: other friends Arata Minase, a champion diver; and musician Reon Yagami; as well as Durak rivals Kiyotada Jokawa, Durak leader; Hayato Chiba, martial artist; and Eiji Sonoda, chef extraordinaire.

Yuki must uncover and overcome a conspiracy; forming a partnership and, potentially, a relationship with a fellow student to save not only his position as council president, but the whole of Bell Liberty Academy.

Keita Itō receives a Platinum Paper, the special letter of admission from Bell Liberty Academy, a prestigious all-boys school that only accepts the cream of the crop.

Indeed, Kazuki rejects many of Kuganuma's proposals and seemingly "abuses" his power by admitting a student of no particular skill — in this case, Itō Keita — to BL Academy.

A short time after winning the MVP Battle, Keita is invited out by the school nurse, Dr. Jin Matsuoka, who takes him to an abandoned building.

Kazuki and Dr. Matsuoka struggle, but in the end Keita wins the doctor over, offering himself as a research subject for the development of a new vaccine that can help Hiroya.