The battle for succession that continued for three generations of shogun in the Keichou era culminated in a gruesome battle of ninja arts between the Kouga and Iga clans. Amidst a rain of flower petals, a man and woman who had decided to live for love were separated once again, beautiful in their transience. However, it is said that by the hand of Hattori Hanzo's adopted son, Kyouhachirou, these two flower petals, whether temporarily or permanently, were given life again and left two mementos behind. These children, born with a destiny of their own, were called Kouga Hachirou and Iga Hibiki. The former had eyes like his father's, and the latter had eyes like her mother's. It is now the Kan'ei era, and the land is at peace. As ninjas begin to disappear into the shadows after being deemed unnecessary, The Kouga and Iga clans ask a favor of Hachirou and Hibiki in hopes of reinforcing their foundations.

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.

Gei'in and Kaso search for Kazuma; a mysterious force attacks the Five Treasures; Joujin confronts Tadanaga.

The mysterious but frightening Joujinshuu slash their way through the Five Flowers after slaughtering the Iga and Kouga.

The ninja battle a foe that can conjure up their own illusions; Hachirou must answer the call to battle.

After the Joujinshuu attack, the surviving ninja split up and go into hiding for several years; Hachirou disappears completely.

Hachirou hears everything about Tadanaga's point of view during the unfortunate incident four years ago.

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

Utsutsu and Rui receive help fighting the Rain forces; The ninja convene at their cafe and draw up a plan to spy on the Murakumo using Shaizou's special seeing technique.

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 armour breaks; Gorone attempts to repair it.

The allies attempt to attack Murakumo Castle, but they face some incredibly challenging resistance along the way.

As the attack continues, Utsutsu recalls her origins as a young girl raised in near-isolation, and the awful truth of how she gained her abilities.

Hadaebou makes a move to kill the Lord of Suruga within Murakumo Castle; Joujin attempts to coerce Hachirou and Hibiki to his side.

With the departure of Murakumo Castle, the ninjas try their best to settle into their own ordinary lives.

Murakumo Castle reappears and begins rolling slowly toward Edo; The ninjas see Hibiki enter the castle and decide to break into it.

Tenkai's servant must retrieve Tadanaga from Murakumo Castle or kill him if he doesn't choose to cooperate.

Hadaebou hits a setback in his plan to extract Tadanaga; The ninjas battle a giant; Hachirou seeks out help from a gathering of ninjas.

Hachirou finally ascends the ramp to get into Murakumo Castle; The other ninja begin reconnaissance; Saizou falls victim to Yasha Itaru's Destiny's Passage.

Saizou's sacrifice allows the ninjas to infiltrate Murakumo Castle, but a greater threat waits for them inside.

The ninjas make their way up Murakumo Castle, but Neirichiou gets in their way, determined to kill them all.

Kujaku's secret is revealed just as Joujin meets a grisly end; The Demon King Nobunaga manages to revive.

Hibiki and Hachirou face the Demon King Nobunaga, but their confrontation throws everyone into a strange dimension where laws of space and time begin breaking down.

In an alternate reality, Hibiki and Hachirou have a final showdown with the Joujinshuu and unleash their ultimate technique upon Joujin, determined to end his evil plot.