According to the legend, five hundred years ago, there was an insignificant lord who possessed a mysterious power that drew ayakashi (supernatural creatures) to him. A demon exterminator, Tokimori Hazama, was called upon to protect the lord and his castle. The lord's power stayed on the land even when he had died. Thus, Tokimori founded the Hazama clan, who inherited his techniques, to protect the land for centuries to come. This land is Karasumori.
In the present day, Yoshimori Sumimura and Tokine Yukimura, heirs of the Hazama clan, are the kekkaishi that protect Karasumori. They are ability users (people who can use supernatural powers) who use a technique called Kekkai. Kekkai is a form of magical energy barrier which is primarily used to capture and destroy ayakashi that are drawn to this shin'yūchi. Any ayakashi that stay on the land become stronger. Yoshimori and Tokine are to guard the land from the intrusion of ayakashi who try to "power-up" there.
Yoshimori and Tokine suffered a lot of hardships in their responsibilities to protect Karasumori. The ayakashi they must fight are becoming more and more powerful, but they managed to protect the land with the help from Yoshimori's older brother, Masamori Sumimura, and the Urakai ("Shadow Organization"). The Shadow Organization itself is an organization of ability users that is governed by a council of twelve, consisting of high level ability users.
Over the course of the story it is revealed little by little that the legend is full of lies. The real source of Karasumori's power is Chūshinmaru, an illegitimate son of the Hazama clan's founder, Tokimori Hazama, and the Karasumori clan's heiress. Tokimori used forbidden arts to try to give his son unearthly power, but the plan backfired, and instead gave Chūshinmaru the power to draw people's life force, killing everybody around him. Tokimori was forced to seal his own son beneath Karasumori. However, being alone with no aid Tokimori was unable to completely seal off the Shinkai he created. Which allowed Chūshinmaru's power to leak out, and it is this that draws ayakashi to the land.
In the end, with the help of Yoshimori's mother and Tokimori, Yoshimori and Tokine find a new site for Chūshinmaru by displacing the founder of the Urakai from the domain of a land-god that the founder had taken over. To seal Chūshinmaru, Yoshimori's mother sacrifices herself by sealing the domain with herself inside.