The Irish Parliament having sent over to England the heads of their bill, according to the constitutional rule established by Poyning's Act, the Irish Catholics sent over Sir Nicholas Plunkett to obtain modifications of its provisions. But Plunkett was met in England with such an outcry from the mob and the press as to the alleged atrocities of the Confederate war, and his own former negotiations on the continent, that he was unable to effect anything; while Colonel Talbot, for his too warm expostulations with Ormond, was sent to the Tower. An order of Council, forbidding Plunkett the presence, and declaring that "no petition or further address be made from the Roman Catholics of Ireland, as to the Bill of Settlement," closed the controversy, and the Act soon after received the royal assent.
Under this act, a court was established at Dublin, to try the claims of "nocent" and "innocent." Notwithstanding every influence which could be brought to bear on them, the judges, who were Englishmen, declared in their first session, one hundred and sixty-eight innocent to nineteen nocent. Proceeding in this spirit "to the great loss and dissatisfaction of the Protestants," the latter, greatly alarmed, procured the interference of Ormond, now Lord Lieutenant (1662), in effecting a modification of the commission, appointing the court, by which its duration was limited to an early day. The consequence was, that while less than 800 claims were decided on when the fatal day arrived, over 3,000 were left unheard, at least a third of whom were admitted even by their enemies to be innocent. About 500 others had been restored by name in the Act of Settlement itself; but, by the Act of Explanation (1665), "no Papist who had not been adjudged innocent" under the former act could be so adjudged thereafter, "or entitled to claim any lands or settlements." Thus, even the inheritance of hope, and the reversion of expectation, were extinguished for ever for the sons and daughters of the ancient gentry of the kingdom.
The religious liberties of this people, so crippled in property and political power, were equally at the mercy of the mob and of the monarch. To combat the war of calumny waged against them by the Puritan press and pulpit, the leading Catholics resolved to join in an official and authentic declaration of their true principles, as to the spiritual power of the Pope, their allegiance to the prince, and their relations to their fellow subjects of other denominations. With this intention a meeting was held at the house of the Marquis of Clanrickarde, in Dublin, at which Lords Clancarty, Carlingford, Fingal, Castlehaven, and Inchiquin, and the leading commoners of their faith, were present. At this meeting, Father Peter Walsh, a Franciscan, and an old courtier of Ormond's, as "Procurator of all the Clergy of Ireland," secular and regular, produced credentials signed by the surviving bishops or their vicars—including the Primate O'Reilly, the Bishops of Meath, Ardagh, Kilmore, and Ferns. Richard Belling, the secretary to the first Confederate Council, and Envoy to Rome, submitted the celebrated document known as "The Remonstrance," deeply imbued with the spirit of the Gallican church of that day. It was signed by about seventy Catholic peers and commoners, by the Bishop of Kilmore, by Procurator Walsh, and by the townsmen of Wexford—almost the only urban community of Catholics remaining in the country. But the propositions it contained as to the total independency of the temporal on the spiritual power, and the ecclesiastical patronage of princes, were condemned at the Sorbonne, at Louvain, and at Rome. The regular orders, by their several superiors, utterly rejected it; the exiled bishops withdrew their proxies from Father Walsh, and disclaimed his conduct; the Internuncio at Brussels, charged with the affairs of the British Isles, denounced it as contrary to the canons; and the elated Procurator found himself involved in a controversy from which he never afterwards escaped, and with which his memory is still angrily associated.