In a soba (noodle) shop, Mizu encounters a "flesh-trader" (a purveyor of women to brothels) with a Western pistol. Mizu forces him to reveal the name of the weapons dealer, Heiji Shindo. Ringo, the kitchen attendant, follows Mizu and implores to be taken as an apprentice.

Princess Akemi, the only daughter of the Daimyo of Kyoto, Lord Daiichi Tokunobu, convinces her father to approve of her marriage to Taigen, a young and accomplished samurai. Mizu seeks a meeting with the master of the Shindo Dojo to find out the location of his brother, Heiji Shindo. When the request is denied it leads to conflict; Mizu defeats the students easily. Taigen, who tormented Mizu as a child, is now the dojo's prized champion, but when Mizu defeats him, the master reveals the location of his brother.

In a flashback as a child, Mizu encounters Master Eiji, a blind swordsmith; they recover a glowing blue metallic meteorite. She becomes his apprentice and learns swordsmithing and swordcraft.

In the present, at the behest of a foreigner, Heiji Shindo dispatches assassins the "Four Fangs" to kill Mizu. Ringo discovers that Mizu is a woman.

Reluctantly allowing Ringo to join her, Mizu arrives at a coastal town, seeking to hire a boat to reach Shindo’s island fortress. Shindo and the foreigner plot a 'surprise' for the Shogun in Edo. Taigen pursues Mizu to regain his honor. Because of Taigen's defeat, Akemi's father plans to marry her off to the Shogun's widowed second son and will take her to Edo in five days, despite her objections. She decides to run away in search of Taigen, although her father's retainer Seki catches her and, unable to stop her, joins her instead.

While Ringo participates in the town Hadaka Matsuri festivities, Mizu trains on the cliffs above. She remembers an assassin named Blood-soaked Chiaki, who tricked her and Sword-father into forging him a sword, which broke near the tip during the forging process due to an injury Mizu sustained during a practice duel with Chiaki. The Four Fangs attack, with their leader revealed to be Chiaki, still using the broken blade. Mizu battles the Fangs on the cliff face and kills all four, although she is heavily injured in the process. Taigen, having tracked Mizu down reveals himself and challenges her, to which she complies but suddenly collapses due to blood loss; leaving Taigen hesitant to strike.

Taigen and Ringo take Mizu to shelter at a nearby shrine. Mizu agrees to a contract to duel Taigen once she is recovered. A huge man with a club delivers an invitation to a ‘Tea ceremony’ with Heiji. Though Taigen suspects this to be a trap, Mizu accepts and they both travel to the meeting. Heiji gives Mizu three options: be paid off to renounce her vendetta, be smuggled into Heiji's castle in sake barrels to kill the white man, or refuse and be killed by archers supposedly hiding nearby. Mizu calls Heiji's bluff and cuts off his arm. Taigen and Mizu escape with Ringo's help while being bombarded by hundreds of arrows. Afterwards, Mizu knocks Taigen unconscious and leaves him with Chiaki's broken blade and a note promising to attend their duel at a later time. Taigen is subsequently kidnapped and taken to Heiji's castle.

Seki and Akemi are ambushed by brigands and lose their money and transport. They hire a cart using the last of Akemi's jewelry, but Akemi discovers that they are traveling in the wrong direction. Seki reveals he has enough money to hire a horse back to the palace, and implores Akemi to give up the search for Taigen and accept the marriage which he brought before her father. Akemi angrily rejects the offer and tricks a flesh trader into transporting her instead.

Mizu seeks out Madame Kaji’s brothel to follow up on what Heiji Shindo revealed about how prostitutes enter the castle of Abijah Fowler, the white man she is seeking. Kaji promises to give her the information if Mizu agrees to mercy kill Kinuyo, a deaf-mute girl who was in Kaji's care before being forcibly taken by the local "thousand-claws" mob boss Hamata. After convincing Kinuyo to believe Mizu will protect her, Mizu carries out her task and leaves the scene making Kinuyo's death look like an accident. However, on her way out a boy sees her; Hamata arrives at Kaiji's brothel with his fighters and orders them to kill everyone.

After realizing Akemi has run off, Lord Daiichi sends his men after her. Akemi ends up in the same town as Mizu and sees her with Taigen's scarf, entering the brothel. Akemi persuades the purveyor to trade her there. To prove her competence when tasked by Madam Kaiji with pleasuring a veteran customer with erectile difficulties, she tactfully uses his interest in poetry and her proficiency in the subject to stimulate and bring him to climax. While she's being applauded for her talent she volunteers to serve Mizu in an attempt to drug her.

At the castle fortress, Taigen is being tortured by Shindo for information about Mizu.

Faced with the threat of Hamata's men, Mizu gathers the women of the brothel in the cellar and tasks Ringo with guarding them. Inside the brothel, she starts taking out the thousand claws individually, but one manages to wound Mizu, resulting in her slowly losing strength.

In a flashback Mizu has while being attacked, allegorical with the tale of the first rōnin, Mizu is seen receiving a similar wound from some gangsters, and is later saved by her presumed-dead mother, who goes on to arrange a marriage between Mizu and a disgraced samurai, Mikio. Mizu gradually opens up to her new husband, but when she beats him in a sparring match, he calls her a monster. He fails to help her when soldiers arrive to collect the bounty on her head. Feeling betrayed, she battles the group and kills them. Mikio and Mizu's mother fight over who betrayed Mizu. Mikio stabs Mizu's mother to death. Mizu kills Mikio and leaves. A narrated bunraku puppet theater play intersperses and complements the storytelling, with its female protagonist eventually transforming into an Onryō, a vengeful spirit.

In reality, Mizu is pinned down but manages to summon back her strength, turns her sword into a makeshift Naginata, and kills Hamata’s men. The men sent by Lord Daichi arrive to take Akemi back home and though she pleads with Mizu to help her, Mizu doesn't intervene. Ringo, angered over his master's callous decision, ends his apprenticeship.

Panning out from the frame narrative, Princess Akemi is shown at the Shogun's palace with her teeth blackened to mark her status as a bride.

Mizu follows the instructions relayed by Madam Kaji, finding the underground passageway to the castle littered with the skeletons of women and infants. While trying to unlock the door to exit the tunnel, she accidentally triggers a water trap and just manages to escape drowning, but loses most of her gear. Her covert entrance is blown when a soldier sounds the alarm, interrupting Heiji and Fowler's meeting at the upper level with two of the Shogun's advisers as they conspire to kill the Shogun and his family to take power by force using guns in Fowler's possession.

Mizu proceeds upwards through the palace, sustaining injury from the numerous castle traps and guards. Eventually, she makes it to a dungeon area where she fights her way through released prisoners before stumbling upon the cell holding a badly injured Taigen. She carries him with her till she comes across the giant carrying a club. Mizu defeats him with an explosive that also breaches the outer castle wall. She then climbs to the top of the outer wall while carrying Taigen, and then confronts Fowler. He shoots at them, injuring Mizu and breaking her sword in two. While Fowler is trying to kill Taigen, Mizu grabs him and jumps into the freezing water below where a hand extends towards them as they are about to drown.

Ringo saves Mizu and Taigen, bringing their unconscious bodies to Sword Father’s hut. While recovering, Mizu's relationship with Taigen starts taking a non-combative and suggestive turn. This comes undone when she reveals Akemi's marriage to the Shogun's son, and of Fowler's impending attack on the Shogunate. Taigen rejects Mizu's broken blade and leaves for Edo to save Akemi and warn the Shogun, vowing to kill her when he returns. After multiple failed attempts and an epiphany that results in mending ties with Ringo, Mizu manages to recreate the metallurgy of her sword's steel but refrains from reforging it until she has slain Fowler. Mizu and Ringo leave for Edo to save Akemi and kill Fowler.

Akemi is chafing against the restraints of her new position in the Shogunate and endures the machinations of her cruel mother-in-law. She confronts her husband, discovering him to be gentle, despite his reputation (the result of propaganda), and also insecure—and pliable—due to his severe stammer. She strikes an understanding with him which leads to the consummation of their marriage. She uses her newly gained wealth to hire the prostitutes of Madam Kaji’s brothel as her new attendants. One of these, Ise, informs her of Fowler's plans which they relay to Akemi's father Lord Daichi, who to Akemi's horror kills Ise, revealing himself to be involved in the conspiracy. He then confines Akemi in a basement cell.

Mizu asks Ringo to wait by the sewers while she saves Akemi and sends her his way. Taigen finds Ringo and they decide to storm the front gate to warn the Shogun about the impending attack, which shortly ensues as Fowler’s army breaks through the castle defenses. Seki saves Akemi from her cell, locking her father in her place, but they are outnumbered by soldiers until Mizu arrives. Heiji opens the final gate from the inside, giving Fowler access to the Shogun and his family. Fowler kills the Shogun, but the Shogun's sons and wife escape after Mizu crashes in, leaving Taigen to kill Heiji Shindo. Mizu subdues Fowler after starting a fire while attempting to stop him from fleeing, which rapidly spreads throughout the castle and then to the city.^[c]

Fowler tells Mizu that they'll have to travel to London to find the remaining two white men, Skeffington and Routely, and that the woman she thought to be her mother was actually a maid paid to raise her. Seki and Akemi shut the front gate of the castle, preventing Fowler’s men from escaping the roaring fire but Seki is fatally shot. Taigen finds Akemi outside the castle and offers to run away with her, but she declines, choosing to remain in Edo with the Shogun's surviving family and her father, Lord Daichi. Ringo returns to Sword Father, convinced that Mizu has perished in the fire. Mizu leaves on a ship for London with Fowler as her captive.