Sanosuke makes his way to Kyoto while trudging through the forest and getting lost at the same time. On the road there, he meets Anji Yukyuzan, a fallen monk currently in training. Sanosuke witnesses Anji unleash an astonishing strike up close, a technique that took Anji 10 years to acquire. There, Anji decides to teach Sanosuke “the Mastery of Two Layers,” an art of destruction. However, he requires Sanosuke to learn the technique within one month; if he fails, he will have to die. Against this unreasonable and excessive condition laid out to him, Sanosuke declares he’ll learn it within a week. The training for this technique, which will make or break his life, begins….

Going back in time, the 4th year of Keio. Kenshin is suffering from a high fever in the main hall of a desolate shrine. Kenshin falls asleep and when he awakens, he finds himself being nursed back to health by former private detective Giichi and his wife Satsuki in their home.

Kenshin undergoes training so that he can learn the ultimate technique. He barely manages to get in a hit against Seijuro in a bout, where he then learns "Kuzuryuusen,"a powerful technique that launches nine slashes at the same time. Kenshin learns to see through Seijuro's swift sword movements and masters "Kuzuryuusen" by looking at it only once. However, the technique was only born out of the process of passing down the ultimate technique, "Amakakeru Ryuu no Hirameki" of Hiten Mitsurugi-ryu.

It is now midnight. Goichi and the others start moving as it is time to put the Great Kyoto Fire plan into action, when they witness Shishio's other underlings being chased by the police. Henya is annoyed that the fires haven't started on time. Meanwhile, an order is dispatched to the Ten Swords, and they start moving upon hearing their orders. Behind the scenes, Kenshin and the rest arrive at Osaka Bay only to come across something.

The engine room of Rengoku. Hoji manages to catch the explosives and prevents the room from blowing up. However, Sanosuke delivers the Mastery of Two Layers to the ship's Kingston valve, flooding the perimeter. Meanwhile, Usui reveals himself to Kaoru, Yahiko, and Misao as Arato faces off against Kamatari and Henya. Goichi begs for Megumi's help at her clinic to heal Tokuji, his younger brother. As these passions clash with each other in all places of Kyoto, a small, over-looked fire begins to flare up.