After the Battle of Sekigahara, a samurai is tasked by the Tokugawa shogunate to raise a band of assassins to finish off Toyotomi's allies and other ambitious warlords, to prevent another civil war.
Azumi (played by Aya Ueto) is discovered as a 7–8 year old girl kneeling without visible emotion next to the body of her dead mother by the samurai master Gessai, played by Yoshio Harada, and his entourage of young students.
Azumi is raised in the martial skills of samurai and shinobi sword fighting, and the art of assassination. Azumi and her fellow classmates, now at young adult age, are constantly being told about a "mission" they must accomplish, though they have no idea what this mission is yet.
Prior to setting out on their mission, their master orders his students to "pair up" with each others' best friend and proceed to kill each other, thus out of 10 students only five will remain to proceed with the mission. Questions and internal conflicts begin to arise amongst Azumi and her comrades as it seems their mission even prevents them from saving a village of mostly women and children from being massacred at the hands of a group of bandits, as their primary mission is to kill the warlords Asano Nagamasa, Masayuki Sanada and Kiyomasa Kato.
Aside from the warlords, Azumi must also deal with a narcissistic mercenary, Bijomaru Mogami, whose sword has no hand guards as he claims to never have had to defend against attacks.
He is very feminine in appearance, seen wearing makeup, having long hair and always carries around a rose. He kills one of Azumi's friends and is the final villain that Azumi has to fight in the movie. Azumi and Bijomaru fight to a standstill when Bijomaru, already insane, snaps. He becomes reckless and Azumi decapitates him.
Azumi 2 continues shortly after the end of the previous film with Aya Ueto returning in the title role of a young assassin charged with keeping the nation from falling into civil war. Her main opponent is a daimyo named Masayuki Sanada (Mikijiro Hira) who employs a special ninja squad.
After the end of Azumi, Azumi and her only remaining colleauge Nagara find themselves hunted for the assassinations they've carried out. After a battle with ninja recruited by Kiyomasa'a retainer, Kanbei, Azumi and Nagara escape and hide temporarily in a temple so Nagara can heal.
While Azumi goes to buy food, she comes across some bandits in a teahouse led by Ginkaku, a young bandit who bears a striking resemblance to Azumi's former friend Nachi.
Later Azumi and Nagara are found by ninjas working for tessai the priest, upon whose orders the assassins intially began their mission. After discussing with Tessai, Azumi and Nagara leave to seek out their final target, Masayuki Sanada. A group of government ninja also accompany them, among them Kozue (Chiaki Kuriyama).
Meanwhile Kanbei assembles a large force of mercenaries and bandits to try and take down the assassins. Amongst them are Ginkaku and his brother, Kikkaku.
After ambushing Azumi and the others in a deserted town, kanbei's ninjas attack but Ginkaku and the others change sides in order to protect Azumi. The ninjas, including their leader, are killed. Azumi and the others return to Ginkaku's family, where they are looked upon with distaste for their occupation. Azumi is torn by her attachment to the Nachi-resembling Ginkaku, but on Nagara's urging they depart.
While travelling, Kozue convinces Nagara that Azumi no longer wishes to fulfill her mission and should be talked out of it. Nagara tells Azumi he is fed up and wants to start a new life with Kozue, and that Azumi should go and live with Ginkaku, and they part ways.
Azumi, still intent on carrying out the mission, attempts to locate Masayuki in his mountain temple only to discover he has left with his army to kill Tessai.
Meanwhile Tessai and his entourage have departed for safety, but are soon tracked down by Roppa, a member of the bloodthirsty Ueno Koga clan working for Masayuki. Most of Tessai's guards are killed until Azumi arrives, as do Ginkaku and his brethren who had been following her. Roppa is killed, as are Kikkaku and several of Ginkaku's brothers.
Meanwhile, Nagara and Kozue begin their search for Masayuki, but once they are alone Kozue reveals herself to be a hidden member of the Ueno Koga clan and kills Nagara.
Coming across Azumi later, she tells her that she and Nagara were separated. However when she attempts to kill Tessai Azumi, realising the truth of Nagara's fate, kills Kozue. Then in anger she states she will go after Masayuki alone. in the forest, Tsuchigumo, another Ueno ninja attacks Azumi and leads her into a trap of poisoned wires. Tsuchigumo is killed after Ginkaku took the thrust intended to her but Azumi is cut and falls into a paralytic sleep. For some unknown reason, Ginkaku managed to dampen the poison on Azumi and he died afterwards.
When Sanada heard about Tsuchigumo's death he became enraged an is eager to kill Azumi by herself, so he decided to challenge her to a one on one duel. Sanada also stated that whatever the result of the duel is they will no longer bother the Tokugawa regime ever again. Azumi, saddened by the death of her loved ones, accepted the duel. During the duel, they appeared to equal each other in terms of skill until Azumi broke Sanada's spear. Sanada took another weapon, but got slashed even before he managed to use it. It appeared that he already received the blow during the time his weapon got broken, but the wounds did not took effect immediately. The duel concluded with Sanada's death and Azumi, being unable to escape her destiny to kill, decided to leave the place to live alone.