"OniAi" centers around Akito Himenokōji, a high school student who lives alone after his parents moved abroad for work. His solitary life takes a dramatic turn when his long-lost twin sister, Akiko, suddenly reappears and moves in with him. Akiko, who has been separated from Akito since childhood, exhibits an intense and overly affectionate demeanor, often blurring the lines between sibling love and romantic interest. Her return disrupts Akito's quiet existence, as she insists on rekindling their bond in ways that make him increasingly uncomfortable.

The story expands with the introduction of other characters who complicate Akito's life further. Anastasia Nasuhara, a childhood friend and self-proclaimed fiancée, re-enters the picture, creating a love triangle as she competes with Akiko for Akito's attention. Meanwhile, Arashi Nikaidō, a classmate and close friend, harbors her own feelings for Akito, adding another layer of tension. The dynamics between these characters are further influenced by the Himenokōji family's peculiar history, which includes a tradition of arranged marriages and a mysterious organization known as the "Himenokōji Foundation."

As the series progresses, the narrative explores themes of familial bonds, unrequited love, and the complexities of relationships. Akito struggles to navigate the conflicting emotions and expectations of those around him, while Akiko's overbearing affection and Anastasia's persistence create a series of comedic and dramatic situations. The story balances lighthearted moments with underlying emotional depth, particularly as Akito grapples with his feelings toward his sister and the other women in his life.

The series also delves into the backstory of the Himenokōji siblings, revealing the reasons behind their separation and the role of the Himenokōji Foundation in their lives. This organization, which oversees the family's affairs, adds an element of intrigue and mystery to the plot, as its motives and influence remain ambiguous. The interplay between the characters' personal struggles and the broader family dynamics drives the narrative forward, culminating in a mix of comedic, romantic, and dramatic resolutions.

Overall, "OniAi" presents a story that intertwines sibling relationships, romantic entanglements, and familial intrigue, set against the backdrop of a high school environment. The interactions between Akito, Akiko, Anastasia, and Arashi form the core of the series, with each character contributing to the evolving dynamics and emotional stakes of the narrative.