"Recently, My Sister is Unusual" centers on Mitsuki Kanzaki, a high school girl whose life takes an unexpected turn after the spirit of a deceased girl named Hiyori Kotobuki attaches itself to her. Hiyori, who died before fulfilling her wish to confess her love, is unable to move on to the afterlife. To help her pass on, Mitsuki must assist Hiyori in completing her unfinished business. However, the situation becomes complicated when a "spirit bridle" appears on Mitsuki, forcing her to comply with Hiyori's demands. If Mitsuki resists or fails to cooperate, the bridle tightens, causing her physical pain.

The story explores the dynamic between Mitsuki and her stepbrother, Yuya Kanzaki, with whom she shares a strained relationship. Hiyori's presence exacerbates their interactions, as her ghostly interference often leads to awkward and embarrassing situations. The narrative delves into themes of family, unresolved emotions, and the challenges of communication, as Mitsuki and Yuya navigate their complicated feelings for each other while dealing with Hiyori's antics.

As the series progresses, Mitsuki and Yuya grow closer, with Hiyori's influence pushing them to confront their true emotions. The plot balances comedic moments with emotional depth, particularly as Mitsuki struggles to balance her own desires with the responsibility of helping Hiyori. The series also introduces secondary characters, such as Mitsuki's classmates and friends, who add layers to the story and provide additional context for the main characters' development.

The anime blends supernatural elements with slice-of-life and romantic comedy, creating a narrative that is both lighthearted and introspective. The interplay between Mitsuki, Yuya, and Hiyori drives the plot forward, culminating in a resolution that addresses Hiyori's unfinished business while also exploring the evolving relationship between Mitsuki and Yuya. The series maintains a focus on character growth and emotional resolution, offering a mix of humor, drama, and heartfelt moments.