The second season of .

The Mizuchi bloodline has long been hunted by Yokai, or monsters. Toru and Noboru Takagami are descendents of this bloodline, and under their grandmother's discretion, are given a secret weapon to combat these monsters. It is Tenko Kugen, a fox deity who can take the shape of a man or woman at will. The mischievous deity is accompanied by a shrine maiden, Ko, who will both live with the Takagami brothers at their house. Life just got complicated.

In the far future, the elevated irradiation from the sun has destroyed the environment of the earth and the birthrate of humans has drastically decreased. The government controls society with an army of cloned soldiers called "Ideal Children (IC)". Sam Coyne is a trader in a desert. One day, he saves a beautiful woman Maya, who has been chased by Theseus, a corps of IC. He shelters her in his trade ship, but the destroyers of Theseus surround Sam and Maya.

A.D. 2040—Thirty years have passed since the battle between the Earth and Zentraedi forces changed the lives of both races. On planet Eden, a top-secret project known as "Supernova" is being held to determine U.N. Spacy's next-generation variable fighter. Competing to win the funding are Shinsei Industries' YF-19 and General Galaxy's YF-21. Piloting the YF-21 is Guld Goa Bowman, a half-human, half-Zentraedi. Shinsei receives its new test pilot in the form of the unruly fighter pilot Isamu Dyson, who was once a friend of Guld. Meanwhile, as Isamu and Guld furiously battle to see which of their fighters is superior, a Virturoid Idol named Sharon Apple is to perform her debut concert on Eden. In charge of Sharon is producer Myung Fang Lone, another former friend of Isamu and Guld. When the three meet each other, old disputes spark from a troubled past. Little do they know that their past incidents—along with the Supernova Project and Sharon Apple—will somehow bring them together.