He continued his education in Nagasaki under the direction of German physician Philipp Franz von Siebold, the first European to teach Western medicine in Japan.

It was this same year that Ōmura began his involvement with Kido Takayoshi, a political moderate who served as a liaison between the domain bureaucracy and radical elements among the young, lower-echelon Chōshū samurai who supported the Sonnō jōi movement and the violent overthrow of Tokugawa rule.

Under the new Meiji government, Ōmura was appointed to the post of hyōbu daiyu, which was equivalent to the role of Vice Minister of War in the newly created Army-Navy Ministry.

Ōmura sought to duplicate the policies he had previously successfully implemented in Chōshū on a larger scale, namely, the introduction of conscription and military training for commoners, rather than reliance on a hereditary feudal force.

He also strongly supported the discussions towards the abolition of the han system, and with it, the numerous private armies maintained by the daimyō, which he considered a drain on resources and a potential threat to security.

During a council meeting in June 1869, Ōmura argued that if "the government was determined to become militarily independent and powerful, it was necessary to abolish the fiefs and the feudal armies, to do away with the privileges of the samurai class, and to introduce universal military conscription".

A man of strong character, Ōmura had come to entertain such disgust at the cramped military system of feudalism that a story is told of his refusing to talk to a close companion of arms who offended him by wearing his long samurai sword during a conference.

On the following evening, he had dinner at a ryōkan in Kiyamachi in Kyoto with Shizuma Hikotarō, a commander of a battalion of the Chōshū clan, and Adachi Konosuke, a teacher at the Fushimi Military Academy.

Shizuma and Adachi were killed, and Ōmura was seriously injured, with cuts to his forehead, left temple, arm, right finger, right elbow, and right knee joint, and barely escaped with his life by hiding in a bath full of dirty water.

On September 20, he received treatment from Anthonius Franciscus Bauduin, a doctor with the Dutch legation and Ogata Koreyoshi, and was transferred to a hospital in Osaka.

However, as a report to the Ministry of War at the time stated, obtaining permission for the operation from the authorities in Tokyo took too long, and on November 1, he developed a high fever due to sepsis, his condition deteriorated, and he died on the night of the 5th.

[3]Ōmura's assassins were soon apprehended and sentenced to death but were reprieved due to political pressure at the last moment by government officials who shared their views that Omura's reforms were an affront to the samurai class.