Ishikawa Goemon is a promising young ninja under the command of Momochi Sandayu - a famous ninja who fought against Nobunaga Oda. Nobunaga, a warlord who despises Buddhism, is trying to destroy all ninja in his quest to rule Japan. The Momochi ninja learn that a competing clan, the Fujibayashi, are planning to assassinate Nobunaga. Momochi is determined to have his ninja kill the warlord first in order to save face. Goemon is made Momochi`s assistant. Although his father does not want Goemon to live the dangerous and often short life of a ninja, he accepts the position and works hard to please his master.

We learn that Momochi has a secret identity. Goemon`s father is killed in an explosion at the hut where he makes gunpowder and we also learn that Goemon is having an affair with Momochi`s wife. The affair is discovered and in a rush to escpape the village, Goemon kills one man and accidentally pushes Momochi`s wife into a well. Momochi intercepts Goemon and says he will spare Goemons life if he will travel to Kyoto, become a thief in order to gather "resources", and assassinate Nobunaga. Fujibayashi tells his clan that they cannot lose face by allowing Goemon to get to Nobunaga first.

Goemon begins his thievery and hands the majority of the money over to his contact who states that he is spreading word around town about the burglaries. Goemon realizes that he is being watched at all times and becomes depressed. Drowning his sorrows one evening, he meets a young woman named Maki who is repaying a debt through prostitution. They spend a lot of time together and fall in love. Goemon reveals his true identity to Maki, but she does not care who he is. One day, the ninja-thief is attacked by two Fujibayashi ninja. He manages to kill them but he is haunted by the killings and by the constant surveillance. Upon his return home, he gives some of his money to Maki and asks her to marry him and move far away. As the girl leaves to pay her debt, Goemons ninja contact comes to remind him of his missions and to say that Nobunaga is going to be nearby that evening. Goemon slips away to carry out his mission and leaves Maki heartbroken.

Goemon is detected while sneaking into the mansion where Nobunaga is staying. While he hides from his attackers, he runs into Hata, the wife of the man he killed while escaping the village. Hata explains that it was actually Momochi who killed his own wife with a poison dart all those years ago. She also confesses her love for Goemon before they both realize that it was Momochi who caused the explosion that killed Goemon`s father. Hata helps Goemon escape and he returns to the village to confront Momochi. Nobunaga massacres all the inhabitants of Ishiyama`s fortress and Fujibayashi decides to attack Nobunaga before he can invade all of Iga.

Momochi escapes and Goemon and Maki move to the country to live a simple, quiet life. While gathering food, Goemon meets up with Momochi who threatens to have Hata killed if Goemon does not agree to kill Nobunaga in Azuchi. Under duress, Goemon agrees to kill Nobunaga with the poison that Momochi gives him. Goemon enters the castle where Nobunaga is sleeping and uses a string to lower the poison into his opened mouth. However, he is only made ill by the poison and even with the help of Momochi`s most powerful kuji, he soon recovers and begins the invasion of Iga. Learning that Nobunaga is not dead and that an attack is imminent, Goemon rushes to the village, which is under attack, to find Fujibayashi and his wife dead in the Momochi home. Realizing that the two are the same man, and that he is freed of his obligations, Goemon returns home.