Tenchu: Dark Secret takes place after the events of Tenchu: Birth of the Stealth Assassins (the second game in the series, but the first chronologically). The plot revolves around Princess Shizu, a young woman who is married to a cruel warlord named Lord Hakkaku. After an attempt on her life, she is discovered by Rikimaru and Ayama of the Azuma Shinobi Ryu ninja clan. They vow to protect her from further harm and discover the identity of her mysterious assailant.

Ayame, a young ninja prodigy who excels at stealth attacks. Though calm and collected on the battlefield, she can be a pain off of it. Rikimaru, an experienced ninja and the leader of the Azuma Shinobi Ryu ninja clan. As a perfectionist who has dedicated himself to the art of war, he can hold his own in face-to-face combat. Kagemasa Hakkaku, the evil warlord of Hakkaku. His lust for power makes him feared by all. Princess Shizu, Kagemasa Hakkaku’s wife. She holds a mysterious secret that could destroy Ayame and Rikimaru. Akunosuke Murai, the fallen general of Toda who now leads a group of mountain bandits. Kurokaze, a mysterious ninja whose skills are feared throughout the land.