[3][4] In January 1922 Pilkington made clear his opposition to the IRAs General Headquarters (GHQ) support for the Anglo-Irish Treaty "We intend to cut away from this headquarters, all of you (pointing to the staff and officers of the GHQ) want to build up a Free State Army so you can march in step into the British Empire.
"[5] On 6 April 1922, a meeting addressed by Arthur Griffith in Sligo, had been proclaimed illegal by Pilkington, who was the local Anti-Treaty IRA divisional commander.
[6] On 4 September 1922, an Anti-Treaty IRA unit under Pilkington took the Dromhaire barracks in County Sligo after the Free State garrison surrendered.
On 27 August 1923, Pilkington ran unsuccessfully in the general election for the 4th Dáil as a Republican candidate, polling 2089 first preference votes.
Aiken proposed that peace should be made with the Pro-Treaty Government on the basis that "The sovereignty of the Irish Nation and the integrity of its territory is inalienable".
In 1954 he was guest of honour at a dinner sponsored by Clan na Gael and the IRA Veterans of America in New York where he said he was returning to the mission fields of Africa, but he remained faithful to the All Ireland Republic.