"Shrine of the Morning Mist" centers around Yuzuru Hieda, a high school student who moves to the rural town of Taga to live with his older sister after their parents pass away. The town is steeped in folklore and mysticism, with the local Taga Shrine serving as a focal point for supernatural occurrences. Yuzuru quickly becomes entangled in the shrine's affairs, discovering that his family has a long-standing connection to the shrine and its guardianship over a mystical artifact known as the "Morning Mist Sword." This ancient relic is said to protect the world from malevolent spirits and maintain the balance between the human and spiritual realms.

The narrative unfolds as Yuzuru encounters various characters tied to the shrine, including the shrine maiden Sakaki, who wields the Morning Mist Sword, and her younger sister, Tamaki, who possesses a mysterious connection to the spirit world. Together, they face threats from vengeful spirits and dark forces seeking to exploit the sword's power. As Yuzuru learns more about his family's legacy, he begins to uncover hidden truths about the shrine, the sword, and his own role in safeguarding the balance between worlds.

The story blends elements of mystery, action, and supernatural intrigue, with a focus on the relationships between the characters and their shared responsibility to protect the town from otherworldly threats. Themes of duty, heritage, and the clash between tradition and modernity are explored as Yuzuru navigates his new life in Taga and grapples with the weight of his family's legacy. The series maintains a steady pace, balancing episodic encounters with spirits and a broader narrative arc that delves into the origins of the Morning Mist Sword and the true nature of the forces threatening the town.