Orphaned in 19th century war-torn Tokugawa Shogun period of Japan, Azumi is found and raised along with nine other orphans by Ji, the mentor. The Shogun, sickened by innocent lives lost in senseless warfare, had commissioned Ji to cultivate assassins that could eliminate warlords before they could strike.

After 10 years of inconceivably harsh training and discipline, Azumi and her comrades, who have been molded into invincible warriors, excitedly await instructions from Ji. "An assassin has no choice but to fulfill his mission, however cruel or extreme," says their mentor. "This is your ultimate test. You must kill your partner, or be killed."

Azumi is stupefied. She and her partner, Nachi, who have developed a special relationship, have no choice but accept their terrible fate - only one of them can survive. With heavy hearts, Azumi, along with the four other survivors of the "test," Ukiha, Hyuga, Amagi, aand Nagara, venture into the vast world outside of their secluded valley.

Their first mission is to assassinate the powerful warlords Nagamasa Asano and Kiyomasa Katoh - rebel heads of the old Toyotomi force. The group's journey leads them to Yae, a beautiful traveling entertainer who captures the heart of Hyuga. For a brief moment, their spirits are lifted and burdens lightened.

However, the supposedly assassinated infamous warlord Kiyomasa had been cleverly replaced with a double. His comrade enlists a cadre of counter assassins to eliminate Azumi and her friends. Yae and her crew who are traveling with Azumi, are mistakenly attacked.

Burdened with the cruel mission to kill friends and enemies alike, sacrificing innocent lives, Azumi begins to question her fate. But Kiyomasa leaves them neither room nor time for self-doubt as his trap ensnares them. Azumi and her friends forge ahead, unaware of the terrible bloodshed that awaits them…