In an alternate 21st century, the ancient Tokugawa Shogunate is at the seat of power. An ominous shadow looms over Great Japan, and threatens to engulf the empire whole. Muneakira, a noble samurai summoned by the Tokugawa clan to take over the Yagyu dojo, finds himself as the bearer of an amazing power that he can't control. Things get even crazier when a girl falls from the sky, right onto his lap, and becomes a Master Samurai! Who is she, where did she come from, and why is she so strong? The power is up for grabs as sexy heroines fight to unravel the mystery and save their world on Samurai Girls!
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 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 whomever he kisses into a Master Samurai, and thus the game begins. While she bones up on technique, Sen and Hanzo lie in wait, ready to stop her no matter what!
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. Meanwhile, Yoshihiko's personal assassin has plans of her own, and her job is clear: eliminate Muneakira at all costs!
Hanzo, after realizing how much Sen has changed, wonders if she is still needed. When an invisible enemy attacks, their bond is put to the test, and Hanzo decides she must protect the princess at all costs!
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. A new threat arises, and the shadow looming over Great Japan begins to take shape!
While Gisen has Muneakira trapped in the depths of his own mind, Yoshihiko's return has thrown the girls for a loop...what are his true intentions, and how will the group rescue Muneakira from Gisen's grasp?
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, Muneaikira, 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!