The leader of the Shanghai mafia, Yukishiro Enishi, arrives in Tokyo with a single, destructive purpose: to make former government assassin Himura Kenshin suffer as he has suffered. Alongside allies who each hold their own grudges, Enishi launches a violent assault on the city, beginning with a cannon attack on the Akabeko restaurant, a place dear to Kenshin. A note left at the scene bears the word jinchū, meaning "human judgment," signaling that this is a personal vendetta. Kenshin, who long ago swore never to kill again and now lives peacefully at the Kamiya dojo in the Meiji era with Kaoru Kamiya and their friends, is forced to confront the sins of his past as the attacks continue against the police chief's home and the dojo itself.

The truth behind Enishi's hatred lies in the events of fifteen years prior. During the fall of the shogunate, Kenshin, then known as the ruthless Hitokiri Battosai, fell in love with a woman named Yukishiro Tomoe. Unknown to him, Tomoe was a spy sent to avenge the death of her first fiancé, a man Kenshin had killed who gave him his first facial scar. Despite her mission, Tomoe and Kenshin genuinely fell in love and married. During an ambush by assassins, Tomoe stepped between Kenshin and an enemy, and he accidentally killed her. As she died, she used a knife to carve the second scar on his cheek, completing the cross-shaped mark he carries forever. Enishi witnessed his sister's death and has been consumed by vengeance ever since, believing Kenshin murdered her in cold blood. He seeks not just to kill Kenshin, but to destroy everything the former assassin holds dear, including his friends and the peaceful country he helped create.

As Enishi's forces continue to bomb Tokyo, Kenshin's allies rally to defend the city. Sagara Sanosuke rushes to protect the dojo but is brutally beaten by Enishi, while Shinomori Aoshi and Makimachi Misao of the Oniwabanshu arrive with Tomoe's diary, which holds the key to understanding the past. Even former enemies like Seta Sojiro appear to assist Kenshin, having been moved by Kenshin's words to leave behind his own violent history. In the chaos, Enishi kidnaps Kaoru but cannot bring himself to kill her, as she reminds him painfully of his sister. Kenshin prepares for the final confrontation at Enishi's mansion, determined to find redemption for Tomoe's death. In the ensuing battle, Kenshin allows Enishi to stab him, apologizing to his tormented rival. When Enishi's ally Wu Heishin fires a gun at Kenshin, Kaoru shields him, and Enishi ultimately takes the bullet for her, finally realizing the emptiness of his revenge.

Afterward, Enishi is arrested and sent to prison. Kaoru sends him Tomoe's diary, and reading her final entry, he breaks down, understanding at last that Tomoe died willingly to protect Kenshin and never wanted vengeance. The film ends with Kenshin and Kaoru visiting Tomoe's grave, where Kenshin expresses his gratitude, apologizes, and bids farewell, finally ready to move forward in his life without being shackled by his past.