A light in the sky. A body falling. A kiss. Unimaginable power is awakened, and with it a series of events will unfold that will change Great Japan forever.

Muneakira, Yukimura, and Matabei are apprehended by Sen, and are awaiting their punishment. Meanwhile, Jubei lies dormant, but only temporarily, and everyone is shocked at what happens when she wakes up.

While Sen figures out what to do about the "girl who fell from the sky", Muneakira and the others themselves wonder what to do about her. Jubei, however, seems to have different plans (though she may not know it), and they all start with a kiss...

The power is up for grabs! Yukimura theorizes that Muneakira will turn whoever he kisses into a Master Samurai, and thus the game begins.

With suspicions that his sister is harboring Yukimura, Sen's older brother sends in a spy to discover the truth. Meanwhile, at the dojo, a new enemy appears, and she seems to have a long time grudge on Yukimura...

Sen and Muneakira need answers. A secret operation suddenly turns into a group outing, and in order to infiltrate the Tokugawa database they must both keep it secret form the others.

Hanzo, after realizing how much Sen has changed, wonders if she is still needed.

In order to fill out their ranks, Yukimura and Sen urge Matabei and Hanzo to kiss Muneakira to become Master Samurai, even though the two girls are hesitant to do so. All of that is shoved to the background, however, when a mysterious girl falls from the sky, in the same way that Jubei did...

Yoshihiko makes his long awaited (dreaded?) return. Gisen lets her true colors be known, much to Jubei's dismay.

While the larger picture becomes clearer, Yoshihiko and and his army of genetic freaks go from looming shadow to possible savior of Japan. Meanwhile, Muneakira finds a new power within himself, and along with his trusted Samurai, they steel themselves for the fight ahead.

With Gisen getting closer to resurrecting Amakusa, Muneakira, Sen, Yuki and Jubei must summon all their strength, courage and love for each other to defeat the shadow looming over Great Japan! The end is finally here, and the greatest battle of their lives awaits!