Whatever the effect of Ovidstown on Alymer the destruction of the Wexford/Wicklow forces on Vinegar Hill two days later on 21 June, must have quickened his efforts to seek peace. This he did around 5 July in a message to the Marquis of Buckingham an acquaintance of his fathers. While arrangements were being made the remainder of the Wexford and Wicklow forces under Edward Fitzgerald, Anthony Perry and Father Kearns joined Alymer on 10 July.

The two forces did not agree and split almost immediately, Fitzgerald and some others stayed in Kildare but about 1600 including some Kildare militants marched north in an attempt to rouse Meath and Louth. These efforts proved as fruitless as those prior to their joining Alymer; they were even beaten off at a fortified house in Clonard by twenty seven yeomen. Constantly harried, they were defeated and dispersed by the military. Around 20 July, Perry and Kearns were back in Kildare but were captured and executed at Edenderry on 21 July. On the same day the Kildare forces officially surrendered.

On 5 July, Sir Fenton Alymer made it clear, that the rebel leaders were prepared to sign a full confession of guilt before a magistrate and the people had undertaken to give up their arms in return for a pardon. The leaders were to be spared on the condition of voluntary self-transportation. Sir Fenton clearly expressed his personal views separately in the letter - 'I would much rather they were attacked but to have them offer to surrender and all the others shall deliver their arms humanity must interfere. The value William Aylmer placed on these proceedings and his wish to have an end to it all were indicated by his refusal to join the Wexford/Wicklow men in their quest.

Buckingham wrote a letter to William's father, with the permission of Cornwallis the Lord Lieutenant. A truce was arranged, and with two officers of the Armagh Militia as hostage in the rebel camp near Prosperous, Aylmer and his officers surrendered. The principal officers including Aylmer and Fitzgerald were taken to Dublin and lodged in the Royal Exchange, for examination. They blamed their involvement on the United Irish Directory who induced them to rise under the assurance that all Ireland was to rise on the 23 May.

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