When a five-year old boy, Ietsuna, suddenly becomes the Shogun of Japan, numerous schemes to seize his power begin to hatch. The Shogun's trusted guardian, Hoshina, secretly asks the leader of the exiled Iga ninja clan, Hattori Hanzo, to help protect the stability of the nation.
Under orders from the Kouga clan, a revenge-seeking female ninja, Okou, infiltrates the bathhouse that doubles as the Shadow Warrior's secret base. Meanwhile, a wild Iga ninja causes trouble for Hanzo by refusing to remain in hiding.
A minor clan comes to Edo looking for warriors to help them take over a castle. Hanzo is suspicious that dirty politics are involved, but is convinced by Okou to help lend his arm in battle despite the hopeless odds.
After several loyal courts nobles are brutally murdered, Hoshima suspects a plot against the goverment is brewing in Kyoto. The Shadow Warriors leave Edo to try and stop the conspirators. But will Okou's desire for revenge ruin everything?
Under the guidance of a ninja hunter, the Tokushima clan is secretly gathering weapons and plotting a rebellion against the government. A bloody civil war will break out unless the Shadow Warriors can sneak into enemy territory and disrupt the plot.
The Iga ninja of Nagasaki are accused of running an illegal opium ring to help fund a campaign against the government. Hanzo and the Shadow Warriors venture to Nagasaki's foreign quarter to try and prove their clan's innocence.
A mysterious female thief is targeting Hoshina's allies. The perpetrator is none other than Hoshina's long-lost daughter who has allied herself with his enemies. Hanzo must help repair the rift between parent and child before tragedy strikes.
Against Okou's protests, Hanzo is determined to solve a mysterious spree of deaths surrounding both a brothel and the Imperial court. He uncovers a complex blackmail scheme targeting some of the most powerful merchants and nobles of Edo.
When wildcat female ninja Kirara (played by Etsuko Shihomi of Sister Street Fighter fame) drops into Edo to visit her uncle Hanzo, the Kouga ninja try to draw her into a trap using her old flame as the bait.
Bathhouse employee Oume has been kidnapped and Hanzo discovers that the Kouga ninja are behind it. She is held prisoner while Minaguchi and his reckless younger brother lure Hanzo into a fateful duel with the revenge-seeking Okou.
A ninja clan thought destroyed has returned to wipe out entire villages of Hanzo's iga clan. When Isaburou, an Iga ninja in hiding, is taken captive, Hanzo must find a way to remove him from his enemies' seemingly impenetrable base.
Daihachi and hyouroku catch a gang of burglars fleeing the scene of a crime. The perpetrators are members of the mysterious Tsuchigumo clan whose well-connected leader wants revenge on the Iga ninja for interfering with his schemes.
One by one, members of the Iga clan fall prey to the supernatural powers of a frightening old hag. Hanzo connects these baffling events to a vengeful enemy who once used sorcery against his ancestors.
A trio of villains orchestrates the kidnapping of the young lord Ietsuna. Hanzo and his Shadow Warriors try in vain to rescue the young Shogun before a successor replaces him. But a mysterious clan of evil ninja stands in their way.
Hanzo makes for his ancestral home to gather the Iga clan for an assault on the castle where young Ietsuna is being held captive. Little does Hanzo know that the order has been given to kill the child as soon as he sets foot in the enemy stronghold!
Someone is killing off the servants of the Annaka clan. Daihachi offers to help out a comely member of the clan by delivering and important letter for her, but he gets mixed up along the way with a traveling group of female entertainers in league with the enemy.
A rich old man from the Kansai area comes to Edo with intent to takeover the local businesses, including Hanzo's bathhouse. The Shadow Warriors seek to end his unscrupulous tactics, but discover they may have spies in their midst.
Hidden villages are under attack by the Tenma, a dangerous clan who seeks to destroy the Iga using explosives. Now, a hidden bomb planted in the Kiji bathhouse threatens the Shadow Warriors.
Lovesick men are drowning themselves in the moat of a castle inhabited by Onatsu and Otama, two of the ex-Shogun's mistresses. Hoshina asks Hanzo to get to the bottom of the mysterious deaths, which are smearing Onatsu's reputation.
When the Saijou clan is left without a leader, Hoshina asks Hanzo to help him find the clan's missing female heir. Hanzo's search brings him into conflict with enemies from his past, including the Kouga ninja.
On the run from the Kouga clan, Okou seeks shelter in a remote temple. Meanwhile, Hanzo ventures to the countryside to check up on his Iga ninja. Along the way, he is reunited with Okou and battles a ninja clan who are abducting children.
After unknown thieves try to rob a shipment of government gold, Hoshina sends Hanzo to guard the riches on their way to Edo. Hanzo enlists the help of several Iga ninja in hiding in order to help with the dangerous task.
Hanzo suspects a group of assassins for hire, known as the dark instigators, is behind a series of suspicious murders. After Oume's sister is found dead in a mysterious double suicide, Hanzo must unmask the leader of the killers.
Someone named "the dark lord" is killing important members of the government. Hoshina suspects the martial arts master of the Satsuma clan is involved somehow. Okiri disguises herself as a man to try and uncover the plot.
Still on the run from Kouga ninja assassins Okou discovers that Hanzo's life is in danger and rushes to find him. Back in Edo, three carpenters have been kidnapped to work on a secret project. Hanzo must find out what it is before the young Shogun is assassinated!
A series of burglaries are being carried out with black pistols. After Oume is shot, Hanzo traces the guns to the mountains where a family of bandits live. Orin follows behind, causing plenty of trouble in her wake.
Just as peace seems to have fallen over Edo, the remaining Kouga ninja plan their final assault against the Shadow Warriors. Now Hanzo must stop the enemy from destroying not only the Kiji bathhouse but Edo castle as well!