In 1778 he published Sonorum doctrina rationalis et experimentalis a study, based on experiments, of Newton's theory of sounds.
In 1782 he published De motibus planetarum dissertatio, another study of Newtonian theory, this time on the motions of the planets in eccentric orbits.
In 1788 Dr. Hales resigned as professor having been appointed Church of Ireland rector of Killeshandra, County Cavan the year before, and lived there for the rest of his life.
In 1798 he obtained government troops to regain control of the country around Killeshandra, following the landing by a French army at Killala.
His other works include The Inspector, or, Select Literary Intelligence for the Vulgar and Irish Pursuits of Literature (both 1799), Methodism Inspected (1803–5), and Letters on the Tenets of the Romish Hierarchy (1813).