His first marriage to Catherine O'Neill, granddaughter of Hugh O'Neill, Earl of Tyrone, directly allied him to the Catholic leaders of the Irish Rebellion of 1641. Stewart was duly appointed an officer in the rebel forces by his wife's cousin, the leader of the rebellion, Sir Felim O'Neill of Kinard. It appears that he switched alliances during the Rebellion. he relieved the Fort of Dungannon, and that of Mountjoy Castle, when at point of surrender to the rebels. Attacking the besiegers with a very inferior force, he dispersed them and drove them back into the mountains of Altadesert and Slieugallen. His early activities against the victorious English miraculously managed to escape their notice until twelve years later, by which time he had become a loyal servant of Parliament. He was exonerated from having played any part in support of the Rebellion, and therefore retained both his land and his life.