He decided to negotiate through Randal MacDonnell, Earl of Antrim, who was loyal to him but also held the rank of Lieutenant General of the Confederate Catholic armies.
The Scottish expedition was beneficial to the Confederate Council, in that it would draw the Scots army away from Ulster, which was, at that time, the biggest threat to southern Ireland.
Also some who followed Randall MacDonnell wished to use the expedition to further the claims of their clan relatives in Scotland and attack their traditional enemies the Campbells.
The expedition sailed in late June 1644, from the Port of Passage in County Waterford in three ships—The Christopher, The Angell Gabriel, and The Jacob of Ross—arranged by Kilkenny merchant Patrick Archer.
According to Leith's Memoirs of Scottish Catholics: "gradually the rumour everywhere spread that a cruel, savage and foreign enemy had invaded the country".