After the successful campaign in Anthracite Country, Mother Jones was drawn back to West Virginia, where the UMW had yet to gain a strong support base. On June 7, 1902, a strike began that led to arrests, and to the increased threat of violence on the part of authorities. Mother Jones herself was put on trial, during which the district attorney called her the "most dangerous woman in America." The conservative presiding judge labeled all the defendants as agitators and condemned them to jail, thereby establishing a precedent that would effectively prevent the leadership of any successful strike. The judge suspended Mother Jones's sentence, however, reasoning that he would not make her a martyr.

Despite the union's failure in West Virginia, Mother Jones continued to work for UMW, and was sent to Colorado to unionize workers in the newly developed Rocky Mountain coal industry. Coal production was dominated by large corporations, which built company towns where all economic and political control was in the hands of the corporation. A statewide referendum for an eight-hour day passed with great public support, but the state legislature never enacted the legislation because of the influence of powerful businessmen. This demonstrated to the workers that their elected governments were controlled by business rather than by citizens, which increased support for socialist and anarchist ideologies.

The Western Federation of Miners (WFM), which was founded in 1893, had already begun organizing miners. The WFM's strong tie to socialism was much more radical than the politics of the UMW, which was more open to compromise with businessmen. However, the UMW also began to gain support in Colorado, especially in the summer of 1903, when labor violations infuriated workers and heightened their interest in organizing unions. In the fall of 1903, the WFM decided to fight for the eight-hour day and started a strike in Cripple Creek. This action was endorsed by the local branch of the UMW, and then by the national UMW office. In November, ninety-five percent of the region's miners went on strike. The strike lost some of its impact, however, when the owners of the northern coalmines began to negotiate with the union, potentially jeopardizing the success of the strike in the south.

Mother Jones fought for unity among the strikers, opposing John Mitchell, who supported the settlement in the north. In a moving speech, Mother Jones persuaded the northern miners to continue the strike, but after she left, the miners agreed to settle with the owners. The strike in the rest of the state dragged on for a year, hindered by the northern miners' decision to stop striking and to start supplying coal again. The situation grew worse for the southern miners, and harassment from company officials increased. Eventually, in October of 1904, they went back to work without gaining any benefits. The defeat precipitated dissension within the UMW, and Mother Jones sided with the union's more radical and revolutionary factions. At the age of sixty-seven, she resigned from the UMW, citing exhaustion, illness, and her personal differences with the UMW's executive board.

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