"To Love Ru Darkness" is a continuation of the original "To Love Ru" series, expanding on its harem and romantic comedy elements while introducing darker, more dramatic themes. The story centers around Rito Yuuki, a high school student whose life becomes increasingly chaotic due to his interactions with alien girls. The narrative shifts focus to Yami, a former assassin from the planet Deviluke, and Nemesis, a mysterious being created from Yami's DNA. These two characters play pivotal roles in the evolving plot, which explores themes of identity, loyalty, and the consequences of power.

The series begins with Yami struggling to reconcile her past as an assassin with her desire to live a peaceful life on Earth. Her internal conflict is exacerbated by the arrival of Nemesis, who seeks to manipulate Yami's darker instincts. Nemesis's actions create tension within Rito's household, as she infiltrates his life and disrupts the fragile balance among the girls vying for his affection. The story delves into the complexities of Yami's character, her relationship with Rito, and her growing bond with the other girls, particularly Lala, the cheerful and eccentric princess of Deviluke.

As the plot progresses, the series introduces new antagonists, such as the organization known as "Darkness," which seeks to exploit Yami and Nemesis for their own purposes. This leads to several intense confrontations, blending action and emotional drama. The narrative also explores the dynamics between Rito and the other female characters, including Haruna, his childhood crush, and Momo, Lala's younger sister, who actively schemes to create a harem for Rito. Momo's efforts to bring the girls closer to Rito often result in comedic and romantic misunderstandings, adding levity to the darker undertones of the story.

Throughout the series, the balance between lighthearted humor and serious themes is maintained, with the characters' relationships evolving in response to the challenges they face. The story concludes with resolutions to many of the central conflicts, though it leaves room for further exploration of the characters' futures. "To Love Ru Darkness" builds on the foundation of its predecessor, offering a mix of romance, comedy, and action while deepening the emotional stakes for its characters.