The following month he co-founded the Common Peoples' Newspaper with another Every Morning News journalist, Toshihiko Sakai. This paper's outspoken anti-war stance and disregard of the state's press laws landed its editors in trouble with the government on numerous occasions, and Kōtoku himself served a five month jail sentence from February to July 1905.
His political thoughts first began to turn to a more libertarian philosophy when he read Kropotkin's Fields, Factories and Workshops in prison. In his own words, he "had gone [to jail] as a Marxian Socialist and returned as a radical Anarchist.
In November 1905 Kōtoku travelled to the United States in order to freely criticise the Emperor of Japan, whom he now saw as the linchpin of capitalism in Japan. During his time in the US, Kōtoku was further exposed to the philosophies of anarchist communism and European syndicalism.
He had taken Kropotkin's Memoirs of a Revolutionist as reading material for the Pacific voyage; after he arrived in California, he began to correspond with the Russian anarchist and by 1909 had translated The Conquest of Bread from English to Japanese.
One thousand copies of his translation were published in Japan in March of that year and distributed to students and workers.
This was an anarcho-syndicalist view, and one which, because anarcho-syndicalism was growing in the US at the time, with the founding of the Industrial Workers of the World, showed the American influence clearly.
He followed this speech with a number of articles, the most well-known of which was "The Change in My Thought (On Universal Suffrage)". In these articles, Kōtoku was now advocating direct action rather than political aims such as universal suffrage, which was a shock to many of his comrades and brought the schism between Anarchist Communists and Social Democrats to the Japanese working class movement.
This split was made clear when the relaunched Common People's Newspaper folded in April 1907 and was replaced two months later by two journals: the Social Democrat Social News and the Osaka Common People's Newspaper, which argued from an Anarchist position, in favour of direct action.
Although most Anarchists preferred peaceful means, such as the dissemination of propaganda, many Anarchists in this period turned to terrorism as means of achieving revolution and Anarchist Communism, or at least hitting out against the state and authority. Repression of publications and organizations, such as the Socialist Party of Japan, and "public peace police law", which effectively prevented trade union organizations and strikes, were both factors in this emerging trend in Japan.
In the episode which became known as The High Treason Incident (Taigyaku Jiken), police arrested five Anarchists for possessing bomb making equipment, which was allegedly intended for a plot to assassinate the Emperor.
This was followed by a big wave of arrests of political dissidents, of whom Kōtoku was probably the most well-known and prestigious. Though there was conclusive evidence only against five, on January 18 1911 twenty-six Anarchists were convicted - mostly on circumstantial evidence. Twenty-four of them were sentenced to death, eleven of whom were actually executed - Kōtoku among them. While he may have known of the plot to kill the Emperor in its initial stages, he had certainly distanced himself from it.
His execution was widely regarded as a miscarriage of justice, though in 1965 the Japanese Supreme Court refused a plea to reopen his case and that of the others executed with him and he is remembered as a martyr by Japanese Anarchists and Anarchists world-wide, sometimes being compared with Sacco and Vanzetti.