In Kannagi, Jin Mikuriya's childhood memory of catching bugs and encountering a deity becomes the seed for a school art project called The Tree Spirit. Wanting to bring the wooden statue to school and spend the day admiring his work, he expects nothing more than an ordinary day, but the sculpture begins to absorb the earth around it and suddenly bursts open as a cute girl named Nagi.
Nagi introduces herself as a guardian of the earth and insists that Jin help her get rid of the "impurities" that plague the land. Yet with Nagi's tree cut down and her powers completely drained, she can only cleanse those impurities with a magical wand and whatever strength she has left. As Jin's life becomes intertwined with hers, the two are drawn into a string of daily antics that slowly reveal more about Nagi, her strange condition, and the bond forming between them. Their odd partnership turns everyday life into a mix of comedy, confusion, and quiet warmth as they try to understand each other and the forces surrounding Nagi.