"Gakuen Heaven Endou ver. ~Calling You~" is a manga adaptation of the popular visual novel and anime series "Gakuen Heaven." The story centers around Keita Itou, a seemingly ordinary high school student who receives an unexpected acceptance letter to the prestigious Bell Liberty Academy, a school known for its elite all-male student body. Upon arrival, Keita discovers that the academy is filled with exceptionally talented and attractive students, each excelling in their respective fields. Despite his initial feelings of inadequacy, Keita quickly becomes a central figure in the school, forming close bonds with his classmates.

The narrative explores Keita's interactions with the diverse cast of characters, including the enigmatic student council president, Naruse, who takes a particular interest in Keita. As Keita navigates the challenges of his new environment, he uncovers secrets about the academy and its students, particularly the mysterious circumstances surrounding his own admission. The story delves into themes of friendship, self-discovery, and the pursuit of one's true potential, as Keita gradually realizes that his presence at the academy is not a coincidence but part of a larger, intricate plan.

The manga maintains a focus on the relationships between Keita and the other students, blending elements of drama, romance, and mystery. Each character is given depth and development, with their individual backstories and motivations intertwining with the overarching plot. The series balances lighthearted moments with more serious undertones, creating a dynamic and engaging narrative that keeps readers invested in Keita's journey and the unfolding mysteries of Bell Liberty Academy.