In May 1640, Ormond, Hamilton's brother-in-law, granted him the manor, castle, town, and lands of Nenagh for 31 years. Ormond was appointed lieutenant-general (commander-in-chief) of the Irish army in September. In 1641 Hamilton accompanied King Charles I on his visit to Scotland. At the outbreak of the
Irish Rebellion on 23 October 1641, Hamilton was in England and was suspected of supporting the rebellion as he was Catholic. He was arrested and shortly held at the
Tower of London but was soon released on bail. Jean Gordon, widow of his elder brother Claud (died in 1638), lost her home when
Phelim O'Neill burned Strabane Castle in December 1641. Hamilton, her brother in law, accommodated her and her children at Nenagh. In February 1642 the Knockaunderrig Silver Mine, which Hamilton operated together with Basil Brooke and Sir William Russell, was attacked by local rebels led by Hugh O'Kennedy and his English miners were killed. In March 1646 Ormond concluded the 1st Ormond Peace. It was proclaimed on 30 July in Dublin. In Limerick its proclamation was violently prevented by the clerical party in August. Ormond sent Hamilton to Limerick to talk to the Irish about the need for unity. In May 1646, Hamilton's wife and children left Nenagh and were brought to Dublin for their security. Similar rescues were organised for his mother-in-law,
Lady Thurles, and his sisters-in-law, Lady Muskerry and
Lady Loughmoe. In June at
Benburb the Confederate Ulster army under
Owen Roe O'Neill defeated the Covenanters under
Robert Monro. O'Neill then marched south to Kilkenny as directed by
Rinuccini, the papal nuncio. Leinster and Munster were treated as enemy territory. On 17 September 1646, O'Neill took Roscrea, but Nenagh was not attacked at that time. O'Neill then menaced Dublin in November 1646. In January 1647 Hamilton returned to Dublin with instructions from the king directing Ormond to hand Dublin over to the English rather than to the Irish. Ormond abandoned Dublin in July to the parliamentarians and left for England. Phelim MacTuoll O'Neill stormed Nenagh in 1648, but it was retaken by Inchiquin in the same year by undermining the castle's wall. Hamilton seems to have been elsewhere. In August he was with Ormond in France at the queen's court at the
Château-Neuf de Saint-Germain-en-Laye. On 21 September Hamilton left Saint-Germain with the queen's instructions and brought them to Ormond at
Le Havre where a Dutch man-of-war, sent by
William II, Prince of Orange, lay ready to bring Ormond to
Cork where he landed on 29 September 1648. In January 1649 Ormond appointed Hamilton receiver-general of the revenues for Ireland succeeding to
Lord Roscommon. He was also made colonel of a regiment of foot and appointed governor of Nenagh Castle. Near the end of 1650 when the parliamentarian army under
Henry Ireton was on its way back from the unsuccessful
siege of Limerick to its winter quarters at
Kilkenny, troops under
Daniel Abbot attacked Nenagh Castle, which Hamilton tried to defend. He surrendered the castle end of October or beginning November after the Parliamentarians had menaced to breach its walls with artillery. == French exile ==