He made vigorous efforts to stay the growth of Protestantism, but with one or two exceptions persecution was not the policy of Archbishop Hamilton, and in the interests of the Roman Catholic religion a catechism called Hamilton's Catechism (published with an introduction by TG Law in 1884) was drawn up and printed, possibly at his instigation.
Having incurred the displeasure of the Protestants, now the dominant party in Scotland, the archbishop was imprisoned in 1563. After his release he was an active partisan of Mary queen of Scots; he baptised the infant James, afterwards King James VI, and pronounced the divorce of the queen from Bothwell.
He was present at the Battle of Langside, and some time later took refuge in Dumbarton Castle. Here he was seized, and on the charge of being concerned in the murders of Lord Darnley and the regent Murray he was tried, and hanged on the 6th of April 1571. The archbishop had three children by his mistress, Grizzel Sempill.
