McKee was promoted within the IRA shortly after his release. He became Company Captain and then Commandant of the Second Battalion, eventually being placed as Brigadier of the Army's Dublin Brigade. He was also active as an ex-officio member of IRA General Headquarters Staff - which included Collins, Richard Mulcahy and Russell. He was a prime innovator in the formation of the flying columns along with Mulcahy and Collins. He was Director of Training for this duration, though he was jailed again as a political prisoner in Dundalk Jail, in 1918.