Natsume, who spends his busy days caught between humans and spirits,
unexpectedly reunites with his former classmate Yuki, which brings back bitter memories connected to spirits.
Around that time, Natsume meets a woman named Tsumura Yorie, who appeared in the memories of a spirit whose name he had returned.
She, who knew Reiko, was now living peacefully with her only son, Mukuo.
Natsume finds comfort in his interactions with them.
However, it seems that a mysterious spirit is lurking in the town where the mother and son live.
On the way back from investigating the matter, a “spirit seed” that had attached itself to Nyanko-sensei’s body
turns into a tree overnight in the Fujiwara family’s garden and bears fruit.
Nyanko-sensei ends up eating one of the fruits, which somehow resembles himself—
and astonishingly, he splits into three――!?