In the end, Yoshie merges with her sister Kikue to form the ultimate robogeisha. They manage to trick Kageno to not blow up Japan and instead, destroy his robot-castle. The film ends with Yoshie (who seemed to have perished with her sister in the explosion) imagining herself and her sister as happy, normal geishas.
The film starts out with an assassination attempt on a political candidate by a geisha (that turns out to be a robot) and two scantily-clad women wearing goblin masks. The goblin-clad women violently (and phalically) take out the body guards (notably shooting shuriken out their butts) as the politician is menaced and wounded by the robot geisha who has a circular saw blade in her mouth. Suddenly, another person named Yoshie (Aya Kiguchi) appears, reveals herself as a robogeisha, and destroys the villainous robot.
We go back in time to see Yoshie as a servant for her sister Kikue (Hitomi Hasebe), who is a geisha in training. It is later revealed that the two sisters were orphaned, and though they used to be close (with Kikue being the favorite child), they are now enemies. Yoshie is klutzy and ruins Kikue's performance for Hikaru Kageno (Takumi Saito), the son of the founder of the powerful corporation Kageno Steel. Despite her klutziness, Kageno is impressed with Yoshie's beauty, and becomes more interested when he witnesses her display superhuman strength when threatened by Kikue.
Eventually, Kageno invites the two sisters to his house, where they are captured by the goblin ladies. The two are forced to fight to the death, and after Kikue wounds and actually threatens to kill her sister, Yoshie snaps and knocks out Kikue, once again displaying superhuman physical prowess. Accordingly, Kageno and his father begin training Yoshie to become an assassin for the company along with many other young geisha-type women, and she quickly becomes the head assassin. They are told that Kageno Steel seeks to use them to kill terrorists and other national threats. Kikue, meanwhile, is relegated to the role of servant to the organization.
Nonetheless, Kikue strives to outdo her sister and shows a greater propensity for violence than Yoshie. Eventually, both sisters undergo surgery to become cyborgs (robogeisha), with machine-gun busts and other robotic powers. On their first mission, however, Kikue is severely wounded when she saves Yoshie from being killed by one of their target's bodyguards. Later, Kikue explains to Kageno that though Yoshie annoys her, she still loves her sister. Nonetheless, Kikue will never be able to recuperate sufficiently to serve as an assassin.
Later, Yoshie is sent to kill a group of elderly people and their young caretaker. Her humanity restored by Kikue's earlier selfless actions, Yoshie refuses to kill them. The seniors then reveal that they are the relatives of the Kageno Steel's geisha and goblin assasins, and that Kageno Steel has actually been abducting these girls to serve their own ends. Yoshie confronts Kageno and his father, who confirm the story. Then, the duo threaten to kill Kikue unless Yoshie completes what turns out to be a suicide mission. The other girls also have been inhuman for so long that they decline to return to their families, remaining geisha assassins.
Yoshie's body is recovered by the senior group and she is rebuilt by the leader, who used to work for Kageno Steel. He reveals that Kageno Steel has actually built a bomb they intend to use to threaten Japan into ceding all power to them. The group then heads off to confront Kageno and his father and force them to return their cyborg relatives or reveal the bomb plot to the authorities. At the meeting with the Kagenos, it is revealed that father and son have also robotically modified themselves and they kill most of the senior group. The leader, however, had installed a gun into his leg and uses it to kill Kageno's father. Kageno, now freed from responsibility, activates a protocol that turns his family castle into a giant robot. Kageno reveals that he intends to drop the bomb into Mount Fuji, thus destroying Japan and himself and "freeing" everyone. The robot-castle is wired to mimic Kageno's every move.
Yoshie launches an assault on the robot-castle, defeating her former geisha sisters and the goblin girls (in a battle featuring a butt-sword duel). She confronts Kageno, but is met by Kikui who has been upgraded into a superior model of robogeisha and who has had her mind wiped. Kikui defeats Yoshie. Knowing she has been bested, Yoshie reveals that, in fact, she was her father's favorite daughter because Kikui was actually born to their father's mistress and was looked down upon. Yoshie reminds Kikue that in fact, it was Yoshie who had defended Kikue's honor as a child and then also allowed Kikue to build their false history and become the family geisha. Finally, Yoshie confesses that she loves Kikue. These revelations manage to overcome Kikue's memory blocks and the two sisters reconcile and merge into one ultra-powerful robogeisha.
The new robogeisha confronts Kageno and trick him during their fight to have the robot-castle (which mirrors his fighting moves) stop the bomb from being dropped into Mount Fuji and launch the bomb and robot-castle launch into space. Once airborne, the sisters defeat Kageno, and the bomb detonates, destroying the robot-castle and all inside (including, presumably, our heroes). The film ends with Yoshie imagining she and her sister living happily as real geisha.