With Lord Ieyasu calling Ogen and Danjo - leaders of the Iga and Kouga ninja clan, to demonstrate each elite ninja own abilities. Impressed, Ieyasu declares the battle against the clans to determine the next Shogun.

After the death of both Ogen and Danjo, not knowing they died, Gennosuke and Oboro are planning their wedding that could unite and bring peae to the clans. However, the Iga clan looks forward to the war against the Kouga clan after getting a scroll.

The Iga clan sets out to hunt down and kill Kazamachi, who has the second scroll. With Tenzen leading, some members of the Iga clan plan to make sure no news of the start of war spreads to the Kouga.

Thinking peace will soon come, Gennosuke and Udono celebrate with Oboro and the Igas. However the Iga clan plans to assassinate Gennosuke and Udono during the feast.

The Kouga clan are concerned with Gennosuke stating at Tsubagakure, even they were informed about the peace treaty. They weren't informed about the war that has arise between the clans. Saemon decides to send his younger sister, Okoi to find Gennosuke.

The Kougas now knowing something drastic must of happen at Sunpu, decide to investigate knowing that the Igas wouldn't attack their village if there is peace coming. However, as the Igas return home they see Okoi, one of the listed Kouga Ten, and decide to hold her captive.

As Rousai pestifers Okoi to find out the fighting abilities of the remaining Kougas alive, Koshiro is sent to tell Oboro that she must meet up with Tenzen. However, when Saemon is able to get into Tsubagakure in the disguise of Yashamaru, what he sees will be the most horrible thing in his life.

With Tousai dead and lord Teyasu's ninja scroll lost to the Iga, the plan to rip the Kouga apart unnoticed is slowly falling apart. With her dying words, Okoi tells Saemon the registry's true location. Determined to make it out alive, Saemon will hold up his ruse long enough to walk out with the scroll in his hands and take vengeance for his sister's death along the way.

With the scroll now in Gennosuke's possession, he makes the decision to either engage in war or not. However, with being attacked by Koshiro and the other deadly ninjas, Gennosuke may have a hard time getting out of the village.

Two woman who hate each other and a little boy could possibly be linked to why the Iga and Kouga hate each other this moment..

Gennosuke returns the scroll to the Iga and issues a challenge that if they attack the Kouga village they will annihilated. The people left can travel to Sunpu and join them. Tenzen accepts the challenge

After blinding Gennosuke, Saemon chases after Hotarubi who misleads him by making him follow her butterflies. A battle disrupts between the two.

Saemon, now having the appearance of Nenki, begins to confront Hotarubi. As the Kouga ready themselves to continue on to Sunpu, Tenzen knowing they can not wait for Nenki and Harutobi, leads the Igas across the ocean in hopes of stopping Gennosuke before he reaches his destination.

As the rest of the Igas cross the sea, Tenzen makes an advance towards Oboro, leaving Koshiro torn between his master and the clan leader. With all the confusion this makes for the perfect opportunity for an enemy to make his move.

Still on the sea, Gyobu uses his art to move around freely to take care of the remaining Iga, but Tenzen proves to be a toilsome foe to kill.

At a lighter time before the disintegration of the no-hostlities pact, talk of an arranged marriage stirred the clans, but could one marry a spouse that they have known to be their enemy?

As the Kogas continue their journey to Sunpu, Oboro's hawk flies by carrying a scroll. While two ninjas pursue the hawk, Tenzen makes his move only to find something he did not expect.

As Hyoma and Koshiro battle, it is revealed that Hyoma was Gennosuke's mentor teaching him how to use his ability.

Oboro and Akeginu discovers the lifeless bodies of Hyoma and Koshiro. Thinking that Koshiro was killed by Hyoma, Akeginu repeatedly stabs the already dead body of Hyoma.

Akeginu vows revenge on Kagero after Tenzen reveals that Koshiro was killed by Kagero's breath.

Kagero sets out to kill Oboro, after telling Gennosuke that she killed her wanting gratitude. She however gets caught in a trap caused by Tenzen.

Oboro issues out a challenge to draw Gennosuke out from hiding. Meanwhile, with Kagero captive Tenzen tortures her with needles. Gennosuke finally arrives.

With Tenzen defeated, Gennosuke carries Kagero away. However wanting to be with him she tries to kill him with her poisonous breath. Oboro's eyes are finally open.

The last battle between the Kouga and Iga, determining who will inherit the title of Shogun. Oboro and Gennosuke face each other for the last time.

A decade after the destruction of the Kouga and Iga ninja clans, only two survivors remain in a hidden village. But fate isn't done with the ninjas yet...

Hachirou wants to leave the ninja village and start a new life. He and Hibiki are destined never to be together, and he's terrified of their powers. But the war between the Kouga and Iga may not yet be over...

A dark force descends upon the Five Treasures as they are attacked by a mysterious ninja... or is he a ninja at all?

The slaughter of the Iga and Kouga continues as the Joujinshuu cut a swath through the Five Flowers. Who are they, and what do they want?

The Joujinshuu continue to cut a swath through the ninja, and Hachirou himself is forced to join the fray.

Many years have passed. The surviving ninjas are in hiding, and Hachirou has disappeared. The Joujinshuu have yet to return, but can these days of relative peace last forever?

As the black castle towers in the forest near the tea stand, Hachirou is called to meet Tadanaga, where he learns the truth about Tadanaga's thoughts during the incident four years ago.

The ninjas prepare to storm Murakumo as Hachirou escapes from Suruga's carefully-laid traps.

Hachirou is determined to slay Joujin and his Joujinshuu, but Joujin has deeper plans for the Lord of Suruga than he'd thought.

The local daimyo stages an attack on the Joujinshuu's Murakumo castle. As their massive army is annihilated by the Murakumo's cannons, Tenkai realizes only ninjas can destroy the castle...

As the ninjas prepare for an assault on the castle, Shikibu's armor breaks. Gorone attempts to repair it, but he's vulnerable when he's not wearing it. Then an enemy attacks, and separates him from the group...

The assault on the Murakumo castle has begun, and the first task is to draw away the troops surrounding it. Rui and Shichigen attempt an assault, but the enemy has prepared for their techniques...

The assault on Murakumo continues as Utsutsu's terrible past, and the origin of her techniques, is revealed.

Hadaebou infiltrates Murakumo castle, where he attempts to kill the Lord of Suruga. Joujin tries to get Hachirou and Hibiki to join forces with him.

The Murakumo castle has vanished without a trace, and it seems as if the Joujinshuu have disappeared. The ninjas return to their normal lives, but is everything really over?

Murakumo is back! Now the castle is on wheels and it's slowly heading towards Edo. The ninjas try to break in as Hachirou attempts to flee.

Tenkai's servant infiltrates Murakumo Castle with a mission: to bring Tadanaga back or to kill him if he refuses to leave.

Hadaebou's attempt to retrieve Tadanaga from Mukakumo Castle does not go as planned. Hachirou appears before the gathered ninjas of Kouga and Iga, faced with an enemy he cannot defeat alone.

Hachirou enters the castle at last, as Saizou falls victim to Yasha Itaru's Destiny's Passage.

Saizou is dead, but his sacrifice has allowed the ninjas to proceed into Murakumo at last. But even greater threats await them inside.

The ninjas make their way up Murakumo castle, but they're stopped by Neirichiou. He's still alive, and he wants them dead.

Kujaku's secret is revealed as Joujin meets a grisly end, and the Demon King Nobunaga revives.

Nobunaga revives, only to quickly die again. Then Hibiki and Hachirou are trapped in a bizarre space created by the Joujinshuu's techniques. When they escape, they find themselves in a parallel world.

In a parallel world, Hibiki and Hachirou face off with the Joujinshuu one final time. The Joujinshuu are caught off guard and overwhelmed, but Joujin still has a final trick up his sleeve: a deep connection to a powerful, hidden ninja.