In Confederate politics, O'Neill was a moderate, advocating a deal with Charles I and the Irish and English Royalists as a means of winning the war against the English Parliament and the Scottish Covenanters. In 1648, he voted for such a deal, the Second Ormonde Peace, splitting with Owen Roe O'Neill, who opposed it along with most of the Ulster army. He and several other moderates such as Alexander MacDonnell and Viscount Iveagh left the Ulster army because of their dispute with the hard-liners. In the summer of that year, the Confederate armies fought among themselves over this issue, with the pro-Royalists prevailing.