Kenshin and Misao arrive in Kyoto, where they’re welcomed by Okina, a grandfather figure to Misao. It turns out, Okina is a former member of the Oniwaban Group. Okina offers his help and Kenshin ask him to help find someone for him.

Hoji plans an attack of Aoiya at night using a secret unit, the Owl Clan, in order to capture Okina and catch a hint of Kenshin's whereabouts, but instead the Owl Clan were the ones defeated. Okina challenges Aoshi to a battle via a member of the clan whom he sent back to Shishio's location.

Aoshi injures Okina, leaves Misao behind, and shows up at Aoiya. He asks the Oniwaban Group where Kenshin is. Aoshi's in a ghastly state, but accepts what Yahiko and Kaoru tell him and decides to wait for Kenshin where Shishio is. Okina is on the verge of death but undergoes treatment by Megumi, who has come rushing to Kyoto.

Kenshin and Hajime realize that Shishio has another objective in mind that lies in Osaka. They meet up with Sanosuke there. To stop the Great Kyoto Fire, Kenshin asks for help from everyone at Aoiya via a letter while leaving Ryusaku Arato, the chief of police, in charge of supervising on the ground in Kyoto. Kenshin, Hajime, and Sanosuke head to Osaka Bay on a carriage after they finish their errands. Then, senior police officer, Hikozaemon Omi brings along Juro Kitazawa, a young 11-year-old boy who says he wants to meet with Arato.

Kenshin and Aoshi engage in a battle on the deck of the ironclad Rengoku. Behind the scenes, Sanosuke manages to board the ship and tries to blow up the engine room with the explosives he got from Tsunan. However, Shishio's underlings Hoji, Shuzo, Toshiro prevent him from going any further. Meanwhile in Kyoto, Arato faces off against Kamatari and Henya alone to buy time for the police forces to evacuate.

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.

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Shishio sends a dueling challenge directed at Kenshin, Hajime, and Sanosuke. The duel is to be held the next day on Mt. Hiei, northeast half way up the mountain in a small shrine with a six-storied torii. At Shishio's fortress, Hoji proposes a strategy to Shishio for an "absolute victory," when the Ten Swords assemble there.... And on the night before the duel, Kaoru talks to Kenshin as he stares up into the night sky.