[4] In the spring of 1581 he oversaw his most famous case, the trial of Regent Morton, which resulted in his execution by beheading on 2 June 1581.
Early in May 1584, he was one of the judges commissioned to serve in Stirling at the trial of William Ruthven, 1st Earl of Gowrie which resulted in his beheading on 3 May 1584 for witchcraft.
[5] In February 1593 in broad daylight, John Graham was shot dead in Edinburgh at the foot of Leith Wynd, next to the building known as "Paul's Work", just north of Trinity College Kirk.
[10][11] David Calderwood said that Graham was finished off by Sir Alexander Stewart's French page in revenge for his master's death.
[12] After his death, his wife Janet Murray, was married for a third time to Peter Young, tutor and almoner to King James VI.