Although only 16 years of age when Ulster Protestant Action was set up in 1956, Paisley nominated the east Belfast native to a post on the executive body of the newly formed movement. Doherty also headed up another of Paisley's initiative, the Orange Defence Committee, a group secretly established by Paisley in 1963 but publicly led by Doherty, to co-ordinate opposition to Terence O'Neill within the Orange Order. Paisley had split from the Order three years earlier but Doherty remained a member and so was chosen as leader of the new initiative. A printer by trade, Doherty oversaw the establishment of Paisley's own printing concern. In 1965 he bought a second-hand printing press and set up the Puritan Printing Press, which produced Paisley's literature, including his newspaper the Protestant Telegraph.
Ulster Protestant Volunteers
In 1966 he came up with the idea of establishing the Ulster Constitution Defence Committee as a governing body of twelve leading Ulster loyalists, which was to be connected to the Ulster Protestant Volunteers, a much bigger body of men which claimed to be committed to legality. Doherty was appointed as leader of the UPV after it was set up. Under Paisley's instructions he was to set up "divisions" of the UPV, based on the divisions of parliamentary constituencies, all over Northern Ireland, although Doherty soon came to refer to these as "cells" and gave the embryonic movement a highly militarised structure. Doherty also sought to buy up stashes of guns for the UPV, feeling that they would be needed in a future Paisley-led uprising. He later claimed that Paisley, whom he referred to as "our Moses", had no idea of these plans and argued that he would not have trusted Paisley with the knowledge that the UPV was building up an arsenal. Doherty was soon introduced to James Marshall, who said that he could supply Doherty and the UPV with explosives and a meeting was arranged at which Docherty was accompanied by Billy Mitchell. The explosives would be used in 1969 as part of a series of bombings in which members of the UPV caused small explosions at a Castlereagh electricity station, Silent Valley Reservoir and a further electricity station in County Donegal. Mitchell, who was a member of the Ulster Volunteer Force, dismissed the attacks as minor, claiming that all Doherty had was "a few sticks of weeping gelly an auld farmer would use to blow up tree stumps" but nonetheless the bombings caused an outcry. Doherty had also joined the UVF and introduced other UVF members to Marshall to supply that group with the same bomb-making technology. He procured explosives for the Shankill Road UVF but during the transaction a business card belonging to his associate James Murdock was dropped at the scene and found by the Royal Ulster Constabulary. Doherty was soon connected to the incident and arrested for his involvement. He was sentenced to two years imprisonment on 18 October 1966. The UVF publicly denied that Doherty was a member of their organisation. Doherty was imprisoned in Crumlin Road Gaol. On the day of his imprisonment, Paisley made a speech outside the prison in which he denied all knowledge of Doherty's offences before announcing that Doherty was forthwith expelled from the UPV and the UCDC. His position as UCDC secretary was taken over by Hercules Mallon, whose brother Frank was already treasurer of the movement. Both would later be tried for their roles in the 1969 bombing campaign.