"Missions of Love" centers on Yukina Himuro, a popular high school student who writes a successful online romance novel under the pseudonym Yupina. Despite her fame, Yukina is emotionally detached and views relationships as transactional, a perspective shaped by her cold upbringing. To gather material for her stories, she manipulates her classmates by assigning them "missions" in exchange for favors. Her life takes a turn when she targets Shigure Kitami, a handsome but aloof classmate, to complete her missions. Shigure, however, proves to be more perceptive than expected and uncovers Yukina's secret identity as Yupina.

In exchange for keeping her secret, Shigure demands that Yukina fulfill his own missions, which often involve physical intimacy or emotional vulnerability. This arrangement forces Yukina to confront her own feelings and the complexities of human relationships. As the story progresses, their dynamic evolves from manipulation to genuine connection, though their interactions remain fraught with tension and misunderstandings.

The narrative also explores the lives of supporting characters, such as Mami Nishikido, Yukina's childhood friend who harbors unrequited feelings for her, and Akira Noda, a cheerful and loyal classmate who becomes entangled in Yukina and Shigure's schemes. These relationships add layers of conflict and emotional depth, highlighting themes of trust, vulnerability, and the blurred lines between manipulation and affection.

The plot unfolds through a series of missions, emotional confrontations, and gradual character development, with Yukina and Shigure's relationship serving as the central focus. The story balances moments of humor, drama, and romance, creating a compelling exploration of how two emotionally guarded individuals navigate their growing bond.