Shishio has a very shady past, which is a vast reflection of his present personality. After his predecessor Kenshin Himura was sent into hiding with a young woman named Tomoe under the disguise of husband and wife, he continued the role of the assassin behind the scenes in a very secretive and efficient manner. His discretion proved to be to his advantage shadowing him into little knowledge being known of his existence, even by some of the members of the Choshu and Satsuma clans. He harbored all the key elements of an assassin: speed, accuracy and conviction. He was extremely skilled at what he did, completing each mission with the utmost perfection, more so that his strength stirred intimidation into the hearts of many especially those who came face to face with his wrath.
One of the first to be assassinated by Shishio was Izuka. Kenshin Himura was Izuka’s subordinate and he received jobs from him regarding assassinations that came directly from one of the leaders of the Choshu clan, Kogoro Katsura. Izuka was considered Katsura’s field chief. The Choshu clan and Satsuma clan had an alliance. However, that alliance was broken once the Satsuma clan decided to go through with a plan involved setting Kyoto on fire. Katsura was against it, hence the reason for them breaking ties. The plans were leaked and Katsura lost everything. The Choshu clan and the shogunate eventually went to war and a great number of lives were lost. That was when Kenshin and Tomoe were sent into hiding using Izuka as a messenger between the two. However, Katsura disappeared and was not heard of ever since the incident. Izuka was suspected to be the spy in the midst since the secret operations and whereabouts of both clans were put at risk. And apparently he was since he was found conspiring with the Yukishiros, Tomoe’s family, who were working as envoys for the shogun. He hoped Kenshin’s skills as a swordsman would wane over time making it easier to dispose of him, all done just for money. He never succeeded. Katsura heard of what happened and had him killed. He later informed Kenshin of Izuka’s betrayal and told him of his newly hired assassin. He never introduced him or told him his name, Makoto Shishio.
Shishio continuously risked his life for the sake of the Imperialists only to have them betray him. Defending the shogunate’s power for the promise of money and glory was what he fought for. After the revolution, the government became afraid that Shishio’s barbaric activities would be leaked to the public. They feared he knew too much of their secrets. In addition, it is my belief that they thought he became too strong to control, hence their desperate attempt at trying to silence him. He was hunted down, shot in the head and burnt alive as the cruelest punishment the Mejii could bestow. However, unknown to them until later on, he had survived and he camouflaged in the shadows waiting and plotting anxiously until he could exact his deep-seated revenge. As Shishio stated, the remnants of the flames of hell has been burning inside his body for every single moment since then.