It is summer 1581. A comet streaks across the sky, highlighting a burning village being destroyed by a three-headed worm monster. A girl, Hayami Ayame, and her brother run out of the village. He hands her the family's sacred sword. She accepts it, telling him that she will fight beside him, but he tells her she must keep the sword safe and go to Hyoga and Hagakure, the other two ninja schools. As she escapes her brother goes back to fight the demon and is killed. So begins Ayame's trek to locate the other two ninja clans.
A hooded ninja is attacked by some bandits. She fights them off easily, but cannot defeat their leader. Throwing off her cloak she shows herself as Ayanosuke (Ayame's name masculinized). The leader of the bandits, a red headed swordsman named Hayateno Sakon, is just as surprised he can't defeat her. The two evenly matched warriors clash, and during their battle the other bandits are killed off by demons. Ayanosuke and Sakon team up to kill the creatures, but they just keep multiplying. Then the shinobi (ninja) controlling the demons appears. He is Saegusa Jinnai, one of the seven Oboro, a kegenin (shadow warrior) like Ayanosuke and Sakon. They try to defeat him, but cannot. To everyone's surprise a soft chanting fills the air and the demons stop. Ryoan the priest appears and tells Ayanosuke and Sakon to go to Hagakure and then vanishes.
The pair are now traveling to Hagekure. Ayame tells Sakon she is going to avenge the destruction of her village. Sakon says he hasn't decided why he is going. They are ambushed, but find their attackers are scouts for the Hagakure. Their leader, ogue Ryoma, trusts them right away and takes them to see his father, Lord Genyusai, leader of the Hagakure troops. The Hagakure have heard of the destruction of Hyoga and Kasumi, the other two ninja clans. Ayame survived from Kasumi and Sakon from Hyoga. Genyusai tells the three about their magical weapons, one for each clan. To the Kasumi there is a kodachi (short sword), to the Hyoga there is a magic katana, and Ryoma inherited the halberd of Hagakure. He also tells them of the powerful Lord Oda Nobunage, who is suspected to be behind all the destruction.
They wait for Nobunaga's next move. Ayame wanders out and talks with Kikyo, Ryoma's sister. She wonders why she survived when her brother died, since he was the one who was able to do everything and she was good at nothing. But their talk is cut short by a demon attack. Genyusai is killed and as the Hagakure shinobi fight they realize that it is once again Jinnai leading them. Ayame confronts him. He tries to smash her with his beads, knocking her off the bridge they are on, but she lassoes him around the neck and takes him down with her. She rides him head first down into the ground. Kikyo runs forward, happy Ayame is still alive. Too bad Jinnai is also alive as well. He fires some daggers at Ayame and Kikyo jumps in the way to save her. Ayame kills him, but Kikyo is badly wounded. With Jinnai dead the demons collapse, but the giant worm that destroyed Kasumi now appears and attacks Hagakure. Ayame can only watch as if destroys everything, holding Kikyo's body in her arms. Kikyo tells her to fight, that she'll wait for her, but she cannot survive the injuries and dies. A very angry Ayame walks toward the worm and destroys it with an incredible magic blast from her kodachi. They bury Kikyo after the battle, Ayame swearing to come back one day and join her.
Once again, the comet streaks across the sky. In the war known as Tasho-Iga, the Iga ninja clan is fighting Nobunaga. Ayame and Ryoma have joined the Iga, hoping to lure out Nobunaga and kill him. However More Ranmaru has advised Nobunage not to go. After Iga's troops are routed by Nobunaga's gun-equipped soldiers, Ayame and Ryoma are attacked by Otawa Genzo, one of the seven Oboro. He has the power of illusion and captures them, but they are saved from his magic by another ninja, a woman named Wadato Kayo who looks very similar to Kikyo. She has come from the neighboring Koga clan.
At a meeting with Momochi, the head of the Iga clan, Sakon loudly states that the Koga clan betrayed Iga and are now fighting with Nobunaga. Ayame and Ryoma disagree, supporting Koga because Kayo saved them. Then Kayo comes in to tell the assembled shinobi that Koga did not betray Iga, only a few families had defected, but most of them were still allied with Iga. Momochi agrees saying that he trusts Koga because kayo is actually his younger sister and the Koga and the Iga were once of the same clan. Sakon persists in arguing and tries to walk out, but Ryoma punches him and says he did not intend to die for no purpose. Jimbei, a young ninja, is hte only one who agrees with Sakon. Kayo is of course upset, and Ryoma tries to reassure her (while blushing and generally making a fool of himself, do I sense a crush?) Momochi retells the story of the three swords to Ayame and Ryoma, and says that they were meant to defeat the evil drawn in by the evil star (the comet).
As Iga attempts a failed surprise attack on Nobunaga later that night, Sakon is leaving. He sees Jimbei going off to fight, after all Iga is Jimbei's home and he has to defend it. Sakon doesn't get very far before he is attacked by "Jimbei", an illusion of Genzo's. He is saved by Ryoan, woh's chanting distracts Genzo long enough for Sakon to kill him. Ryoan tells Sakon that he fell for the illusion because he still cared about the friends he left behind.
Meanwhile, Momochi, Ayame and Ryoma return to Iga to find it destroyed. Jimbei, wounded and blinded tells them that Koga betrayed them. He is suddenly killed by a spear in the back. They look up to find Kayo standing on a cliff. Kiro Masago, an Oboro is controlling her and climbs out of her back. Momochi tries to kill Masago, but cannot, sacrificing himself to try and destroy his sister and Masago, and only succeeding in wounding Kayo. Ryoma runs to see if Kayo is all right and is caught by Masago, who turns into a wicked monster. She tearfully tells him to kill her and he grants her wish to be free from the possession. He not only kills Kayo, but Masago as well. Once again, the comet reappears in the sky...
In the late summer of 1583, Ayame and Ryoma make an assassination attempt on Nobunaga, but only manage to kill an imposter. Time is running out for them to kill Nobunaga, and he has become so paranoid by this point that he has killed his own guards, his castle filled with rotting corpses and the only survivor is his advisor Ranmaru. Meanwhile, in Horai cave, Ryoan is trying to convince Sakon to rejoin his old comrades. Sake has become a hermit and is no longer interested in the fighting. He doesn't understand why Ayame and Ryoma are still after Nobunaga.
As Ayame and Ryoma prepare for their final assault, Ayame thinks back to the last time she saw Sakon. She had gone to try and convince him to rejoin them, telling him that it was their destiny to destroy Nobunaga. Sakon questioned her reasoning and that destiny is not worth dying for. He then silences her with a kiss. She slaps him (ouch, what was she thinking!?) and runs off, but he tells her that he does not believe in destiny, nor will he die for it. As Ayame thinks, Ryoma wonders why Ayame gets so quiet whenever he mentions Sakon.
It is nightfall, Ryoma attacks by water and Ayame by land. She is the first to run into an Oboro, Kiheiji (love that name) who ensares her in a web. She manages to cut herself loose but is knocked down. Kiheiji goes to kill her, but a figure suddenly comes into view wearing a fox mask. A strike by the Oboro cuts the mask in two and reveals Sakon. He tells her to go ahead while he fights Keheiji. Ryoan joins Ayame on her way to the castle.
As Ayame attacks, Ryoma arrives at the castle and runs into an Oboro. There are corpses all around and the only one there is a little girl in a kimono playing with a ball, Kagami. He approaches her and she starts crying, animating the corpses. Ryoma kills them all and then Kagami drops the ball and it explodes, knocking Ryoma down. Kagami smiles at her victory, but is then speared through the middle by Ryoma's halberd.
Evil fills the air as Nobunaga begins to change, complaining to Ranmaru that his head hurts, but Ranmaru doesn't care. Ryoan and Ayame are attacked by more demons, so Ryoan tells her to go on alone. Ayame tries to continue, but suddenly looks up to see a giant demon (that would be Nobunaga) breaking through the roof to attack her. Ryoan starts chanting, trying to help her, but a voice says "Your role is finished" and is killed (that was Ranmaru's voice).
Back at the Sakon versus Kiheiji fights, things are not going well for Sakon. He cannot use the sword's power and so the Oboro is having an easy time with him. Sakon is bleeding, then loses his long red hair to a sweep of Kiheiji's sword in a pass. Then Kiheiji spears him in the abdomen. As Sakon collapses his sword flares to life and Kiheiji is killed. Ryoma sees this and even though he is badly injured as well, he sends his halberd's power to Ayame. She uses the combined power of the three magical weapons to kill the Black Demon/Nobunaga.
Ayame is knocked back the resulting explosion and gets up to see the demon gone but Ranmaru is still there. She assumes he is the last of the Oboro, but he tells her that they are all dead. Ryoan was in fact the last of the Oboro. He was programmed to bring the three warriors to that place at that time. Ayame attacks Ranmaru, but cannot hurt him. He tells her that her weapon, in fact all their weapons, were created by him and cannot harm him. Ranmaru is not human, but a demon that descended from the comet over 500 years ago to make a suitable home for his people. His plan had three parts 1) to gather negative human emotions that powered the magic weapons (that's why Nobunaga destroyed everything, why Koga betrayed Iga) and combine them with the power of the Oboro to form the Black Demon 2) wait until the comet was closet to Earth so that the gap from the Earth to hell could be bridged 3) combine the negative emotions and demonic energy to warp the dimension and open the gate to hell.
Ayame can't accept the fact that he manipulated her "destiny". He goes in to kill her now, but Sakon jumps in and takes the blow. He reminds her not to give up; a ninja should fight to the death. She faces Ranmaru again but cannot fight him, so Sakon challenges Ranmaru. But his injuries slow him down as well and he cannot kill Ranmaru. Then out of nowhere Ryoma appears and spears Ranmaru through the back with his halberd. He wants to close the gate to hell with his will - if emotions opened it, their combined emotions could close it. He jumps into the open gate as Sakon and Ayame combine their sword magic with Ryoma's to kill Ranmaru and begin warping the gate in on itself. Ryoma dies too, his last thoughts of his sister Kikyo. Ayame runs forward to watch the gate close, happy it is over, but now Sakon is dying. He reminds her that now she can be a woman again instead of playing the role of Ayanosuke. He had something to tell her, but cannot remember what it is. He mentions that the moon is full and when Ayame looks up into the sky he tells her that it is quiet and dies.
Ayame is left alone once again.
