The story in Ninku is about an odd-looking 12-year-old named Fūsuke (Fūsuke of the wind) who is a powerful warrior from the Ninku school of martial arts, a style that mixes ninjutsu and karate. It is explained that before the present time in the story that those who could use Ninku were targeted by an evil empire and the Ninku corps were formed to combat the menace. The names of the corps were taken from the twelve Chinese zodiac animals (Eto) and each captain of the corps was called the zodiac animal Ninku master (Etonin). When the war was over, the Ninku were defeated and almost all of them were killed since they were useless and were also dangerous for the rulers. At the beginning of the story, three years later, Fūsuke, the young former captain of the 1st Ninku corps and controller of the wind and Hiroyuki, his flatulent penguin, start searching for the other Ninku captains...
Fusuke the Ne-nin!
The Appearance of the Tori-nin Captain
Touji of the Land
The Attackers
The Smoke of Concealment!
The Terrifying Base
Ice of Onjun!
The Sealed Heart
Mother's Lullaby
Sad Parting
The Trial
The Method to Become Strong
A Faraway Promise
Overcome the Pain
True Courage
The Legendary Forest
Ninku Trap!
Desperation!!
Till the Ends of the Battle
Dolphin and Youth
The Hole of Hell
Terror of the Fist
Flame of Sekirai!
Rebellion for Freedom
Father and Son!
Farewell, Hiroyuki
The Valley and Fuusui
The Three Demonic Warriors
The Sky Dragon Appears!
The Shapeless Sniper
Breakthrough the Barrier
The Awakened Sekirai!!
Prologue to Crisis
The Magic that Summons Death
Heroes of the Sky!
The Mysterious Youth
A Departing Promise
Fuusui's Cape
The Crushed Ice!? The Sky Dragon Reappears
Confrontation! The Use of Fog VS The Use of Wind
Rihoko's Tears, Father's Hometown
The Fist of Wrath! The Man who Slashes Ninku
The Horror Building! The Mysterious Haunted House
A Confrontation!? Friendship that Uses Secret Weapons
Miss Ninku! Operation Breakthrough!
Assassin of the Night! The Sealed Technique
To the Capital! The Rebels of Justice
The Revived Memories! The Man who Captured Mother
The Unleashed Power! The Time of Battle
Fuusuke Overcomes Power! The Strongest Ninku!!
The Employed Bodyguard! Duel in the Evening
The Decline of Fuusuke's Adversary! Mystery of the Masked Man
The Stage of Friendship! Hiroyuki's Secret
The Missing Bills!! Who is the Culprit?!
Fuusuke becomes a Movie Star?!