Shishio has set sail in his ironclad ship to bring down the Meiji government and return Japan to chaos, carrying Kaoru with him. In order to stop him in time, Kenshin trains with his old master to learn his final technique.

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.

A scientist uses his invention – the “Menger Sponge” – to capture the energy of a dead child’s spirit in an old building. In trying to determine why the energy of the ghost does not dissipate, the team discovers the identity and the dramatic story of the boy.