Kenshin has settled into his new life with Kaoru and his other friends when he is approached with a request from the Meiji government. Makoto Shishio, a former assassin like Kenshin, was betrayed, set on fire and left for dead. He survived, and is now in Kyoto, plotting with his gathered warriors to overthrow the new government. Against Kaoru's wishes, Kenshin reluctantly agrees to go to Kyoto and help keep his country from falling back into civil war.

Shishio sets sail in his ironclad ship to bring down the government. In order to stop him, Kenshin trains with his old master to learn his final technique.

Set during the Meiji Restoration period of Edo era Japan, Naoyuki belongs to the 8th generation of the Inoyama family, a wealthy family known for finance & accounting. He is also a gifted mathematician and uses the abacus with extreme skills. Naoyuki works under the declining Kaga domain. Because of this, Naoyuki and his wife Koma suffer hardships as their stature and wealth dissipates.