Natsume Yuujinchou San follows Takashi Natsume, a boy who is able to see youkai. Natsume and his bodyguard Madara, nicknamed Nyanko-sensei, continue on their quest to release youkai from their contracts in the "Book of Friends." Natsume comes to terms with his ability to see youkai and stops thinking of it as a curse. As he spends more time with his human and youkai friends, he realizes how much he values them both and decides he doesn't have to choose between the spirit and human worlds to be happy.

The story revolves around a new team of "Toei robot girls" named "Team Z" that is made up of three girls based on Toei's Mazinger Z franchise: Mazinger Z, Great Mazinger, and UFO Robot Grendizer. Usually they perform in activities around Nerima ward in Tokyo to raise the awareness of the promising future energy source "Photon Power" (koushiryoku). However, there are times when "Mechanical Beast" team of girls emerge from the "Subterranean Empire" and attempt to steal the energy. Thus "Team Z" has to battle them to prevent this, though sometimes they just go and beat up the "bad girls" to relieve stress. Please note that because in this particular case MAL lists airings, not episodes/chapters/parts, this show is considered to be 3 episodes and not 9. Each of the three airings consisted of three episodes for a total runtime of 27 minutes per airing. The duration on MAL reflects this.

Human civilization no longer revolves around fire, but is instead now driven by fear of it. Repeated wars have changed human biology, and people now spontaneously combust when they get close to natural flame. However, a new source of energy prevents society from complete collapse: a stone-shaped material used to produce light and steam lies within the bodies of monsters that infest numerous forests. Those tasked with collecting this precious resource are called fire hunters. Touko, a young village girl, is saved from a forest monster by a fire hunter who perishes during his heroic action. After the hunter's dog, Kanata, heals from his own injury, the girl's family sends her to the capital in order to return Kanata and the hunter's fire sickle to his relatives. Elsewhere, the fire hunter's son, Koushi, and his sister are adopted by a wealthy family. Koushi learns some troubling facts related to the country's ruling royal family. He conducts secret research on a special fire stone found by his late father, kickstarting a race against time between the country's leaders and those trying to save mankind from its ultimate demise.

Bonus episodes 3.5, 6.5, and 9.5 included with the Blu-ray/DVD releases.