In 1855 power shifted in California from the Democrats to the American Party, also known as the Know-Nothings, an anti-Catholic, anti-immigrant movement that had subsided in the East, but was still very much alive in frontier California. The shooting of U.S. deputy marshall General William H. Richardson in November 1855 was to set off a chain of events that would lead to McGowan having to abandon California altogether. Richardson was shot by a gambler named Charles Cora following a confrontation between the gambler and an angry, drunken, pistol-waving Richardson who had been angry at Cora because of a public fight between their respective wives.[9] Cora claimed self-defence. James King of William, editor of the pro-merchant, pro-American Party Bulletin whipped the citizens into a frenzy over the possibility that Cora might not be hung for the death of Richardson, and was driven to frenzy when the jury in the trial couldn't reach a decision. The Sunday Times, published by a former Democrat turned Know-Nothing named James Casey, fanned the problem by including a defamatory insert attacking King of William's brother Tom and the morals of his wife, signed "Caliban", a pen-name known to be used by McGowan.[10] Tom King threatened James Casey. Casey appealed to Judge McGowan, who conveniently lent him his knife and Texas five-shooter. When King of William published a story libelling Casey, claiming he had spent time in prison for stealing furniture for his prostitute mistress,[11] Casey and King of William had a run-in which resulted in King of William being shot by Casey with McGowan's pistol. King of William was not gravely wounded in the altercation, but still died a few days later, probably from dilatory medical care. The Committee of Vigilance was reactivated even before King of William died. A veritable army of 2,500 was gathered instantly.[12] The sheriff guarding the jail where Casey was being held called for help in the face of this build-up of the vigilante army, and McGowan was one of those who came forward. However the American Party state governor of California, James Neely Johnson, allowed the Committee of Vigilance access to the jail, and the committee members quickly seized both Casey and Cora. Notes arrived at McGowan's residence advising him that he was next, and when King of William died and Casey and Cora were summarily executed, Ned McGowan went into hiding.
McGowan escaped San Francisco, using a Mexican disguise, and hid out in various parts of California, narrowly escaping the Committee of Vigilance in Santa Barbara, by having himself rolled into a carpet. Eventually his friends managed to have a special act passed in the California legislature to enable him to be tried in the Napa Valley, far enough away from San Francisco to ensure a fair jury. As expected, McGowan was acquitted, and subsequently founded two newspapers, the Phoenix and the Ubiquitous which he used to expose the sordid and criminal backgrounds of members of the Vigilance Committee.[13] However, the Committee of Vigilance remained powerful in San Francisco, and when McGowan tried to leave California in 1858, news of his departure reached committee members and when he reached San Francisco a warrant had been issued for his arrest and one of the police officers, Jim Boyce, pulled a gun and shot McGowan in front of the courthouse.[14] Fortunately for McGowan the bullet had missed, and despite the general hostility of Vigilance-ridden San Francisco, McGowan managed to escape to the harbour and board the Victoria-bound steamer Pacific.