"Rental Magica" centers around the operations of Astral, a magical assistance agency that provides supernatural services to clients in need. The agency is led by Itsuki Iba, a young and inexperienced magician who inherits leadership after his father mysteriously disappears. Despite his lack of magical prowess, Itsuki relies on a powerful artifact called the "Eye of the Horus," which grants him the ability to summon and command skilled magicians from Astral's roster. This artifact becomes crucial in managing the agency's diverse and often dangerous missions.

The series unfolds through episodic arcs, each focusing on Astral's assignments, which range from exorcising spirits to resolving conflicts between magical factions. The agency employs a variety of magicians, each specializing in different forms of magic, such as Honami Takase Ambler, a skilled astral mage; Mikan Katsuragi, a shrine maiden with spiritual abilities; and Nekoyashiki, a cat-like sorcerer. These characters bring unique skills and personalities to the team, often clashing but ultimately working together to solve supernatural problems.

As the story progresses, deeper mysteries surrounding Itsuki's father and the true nature of the "Eye of the Horus" are gradually revealed. The narrative also explores the dynamics between Itsuki and his team, particularly his evolving relationship with Honami, who harbors feelings for him but struggles with her loyalty to Astral and her own personal goals. The series delves into themes of trust, leadership, and the ethical dilemmas of using magic in a world where supernatural and human interests often collide.

The plot intensifies as Astral faces external threats from rival magical organizations and internal conflicts among its members. These challenges test Itsuki's resolve and force him to grow into a capable leader, balancing his reliance on the "Eye of the Horus" with his own developing skills. The series concludes with a resolution to the overarching mysteries while leaving room for the characters' continued growth and the agency's future endeavors.