Adopted by Danjou Kouga, Gennosuke is heir to the Kouga clan and after Danjou's death, their leader. Before the war, he was engaged to Oboro. An idealist who believes that the two clans should put the past behind them, Gennosuke seeks to end the war between Kouga and Iga. Gennosuke has a special ability called Dojutsu which allows him to reverse the murderous intent of others and turn them against themselves, leading them to commit suicide.
Oboro is the granddaughter of Ogen and heir to the Iga clan. When Ogen is killed, she assumes leadership of the clan. Oboro was engaged to Gennosuke Kouga before the war reawakened, and is committed to peace between the two clans. Her passive nature often infuriates her subordinates. Oboro possess an ability known as Mystic Eyes, which allows her to neutralize any ninja skill. Outside of this, she has zero effectiveness in a combat setting due to a lack of combat skills.
Cold and ruthless, Tenzen desires to make himself leader of the Iga and to wipe out the Kouga. He despises Oboro's passive leadership and usurps her position as leader. Tenzen has the ability to almost regenerate even fatal injuries on his body with the help of a symbiotic demon living within his body. As a result, Tenzen is in fact over 200 years old and has been at the center of most major conflicts involving the Kouga and Iga clans.
Gennosuke's uncle Hyouma serves as Gennosuke's second-in-command. Hyouma has the same Dojutsu power as Gennosuke, although is is constantly active. This requires Hyouma to keep his eyes shut at all times, lest he turn his power on the wrong person. Always cautious, Hyouma is Gennosuke's main adviser during the war with Iga.
Akeginu acts as Oboro's bodyguard and is more accepting of Oboro and her shortcomings, but keeps her loyalty to Iga paramount. Akeginu's special ability allows her to secrete her blood from her pores and spew it onto her enemies, creating paralysis. She can also use her blood to make a thick red mist in which to hide.
Saemon Kisaragi can replicate anyone's appearance by pressing their face into mud to form a mold and then putting his own face into the mold. He is also a master of impersonation, imitating even female voices like Akeginu flawlessly. Saemon maintains an air of detachment over the war, and is only interested in claiming victory for Kouga and avenging his sister Okoi who ends up brutally tortured and murdered by the Iga.
Kagerou is largely supportive of the war and harbors a hatred for Oboro, born of her own unrequited love for her cousin Gennosuke. Kagerou is a combat expert, although her sexuality is her deadliest weapon. When sexually aroused, Kagerou's breath contains a lethal poison.
The instigator of the current war, Ieyasu Tokugawa is the retired shogun. Questions of the succession of his grandchildren threaten civil war. He contacts the Kouga and Iga clans and Hattori Hanzo, and instructs Hanzo to break the peace pact existing between the Kouga and Iga. Each clan must select 10 ninjas to represent them in battle, with the last clan standing determining which of his grandsons will become the next shogun.
Saemon's sister Okoi has the ability to adhere her skin to others and drain their blood, while Jousuke Udono's rotund frame has the same properties of rubber and allows him to turn his body into a living boulder. Gyoubu Kasumi can merge with his surroundings, giving him the ability to hide and execute sneak attacks, while the limbless Juubei Jimushi can slither at high speeds like a snake and use his prehensile tongue to grasp objects. Shougen Kazamachi can spit out a stick glue-like substance that he uses to make webs like a spider. Danjou Kouga is an expert at throwing needles, and can use them with lethal accuracy and strength.
Hotarubi can summon butterflies to distract her opponents, and has a pet viper which strikes at foes, while her lover Yashamaru controls steel-like wires to tie up, flay and pierce enemies. Nenki Mino is covered in hair, which he can use to grab opponents, throw weapons and pierce enemies like needles. Jingorou Amayo is able to dissolve himself into a viscous slime, while Koshirou Chikuma can create a vacuum that rips enemies to pieces. Rousai Azuki's has unnaturally stretchy limbs he uses as weapons. Ogen can control her pet hawk, and uses it to deliver messages and spy on enemies.