High schooler Nanami Momozono has quite a few problems of late, beginning with her absentee father being in such extreme debt that they lose everything. Downtrodden and homeless, she runs into a man being harassed by a dog. After helping him, she explains her situation, and to her surprise, he offers her his home in gratitude. But when she discovers that said home is a rundown shrine, she tries to leave; however, she is caught by two shrine spirits and a fox familiar named Tomoe. They mistake her for the man Nanami rescued—the land god of the shrine, Mikage. Realizing that Mikage must have sent her there as a replacement god, Tomoe leaves abruptly, refusing to serve a human. Rather than going back to being homeless, Nanami immerses herself in her divine duties. But if she must keep things running smoothly, she will need the help of a certain hot-headed fox. In her fumbling attempt to seek out Tomoe, she lands in trouble and ends up sealing a contract with him. Now the two must traverse the path of godhood together as god and familiar; but it will not be easy, for new threats arise in the form of a youkai who wants to devour the girl, a snake that wants to marry her, and Nanami's own unexpected feelings for her new familiar.

Evil Shinma (shape-shifting monsters and vampires) roam the Earth on a mission to unleash their darkness upon the Human race. Miyu Royal Princess from the dark is the Chosen One—the one being who must banish the Evil Shinma from the Earth. She has the power to offer Humans the gift of eternal happiness, yet is herself, trapped between two worlds; destined for perpetual solitude and internal conflict. Miyu's only companion is Larva, once an evil Shimna; now her devoted guardian. Together they share a dark journey through the weakness of the human heart and the tragic loss of innocence. Cut off from humanity by the knowledge of what she is, Miyu lives an endless quest as both the hunter and the hunted, on the edge of darkness.

In Ming dynasty, legend goes that there is an ancient deity's book covering a wide range of technical issues, including the unique method of manufacturing the weapons of deity, which has the power to destroy everything. He who gets that book rules the entire nation. Reportedly, in ancient times, deity made the royal family keep the book, as a sign of acknowledging their ruler-ship. However, in Yuan dynasty, the Mongolians invaded the central plain and ruled the nation. There was chaos everywhere and the book which was supposed to be enshrined in the Imperial Palace was somehow missing and reappeared in the outlaw societies, luring lots of forces to fight for it. When Han people regained the ruler-ship in Ming dynasty, though the deity's book was found back and enshrined in the Imperial Palace again, those outlaw forces already knew that the book was more than just a legend! It did exist! So they plotted to steal it out. There are there most famous robbers in the outlaw societies: Hell-fire monk, Hua Daochang the thousand-face fox and Duan Yun in white. One day, on the ghost festival, they sneaked into the Imperial Palace, trying to steal the most precious treasure, competing for the title of "the most famous robber." At last, the hell-fire monk stole the deity's book. The emperor founded the Imperial Guards to serve as his personal bodyguards and imperial secret polices and spies, among whom, there was a young and inexperienced guard—Yuan Xiaotang，the hero of this animation. The emperor demanded the Imperial Guards catch the three robbers and find back the book. That's how the story begun!

Second season of 3D Kanojo: Real Girl.