In March 1572, during the Marian Civil War, he surrendered the castle to the supporters of Mary, Queen of Scots, for 300 crowns, after his expenses had not been met by the King's side.
Alexander Stewart set about bribing the same soldiers and Regent Morton forced James Kirkcaldy's wife Helen Leslie to make him surrender.
[7] Robert Bowes was told in December 1582 that Alexander Stewart, son of the captain of Blackness, knew of plans to destabilize the Ruthven regime, an English-leaning Scottish government.
[14][15] George Young, another negotiator in London, was disappointed by Stewart's conduct as a diplomat, and wrote to William Cecil that he was, "sory in gude faith that he or any Scottisman sould overshute himself sa farre in a mater quhilk I doubt not his majestie will let appeare mair clearlie".
[17] Alexander Stewart became involved in a feud between a wealthy lawyer, John Graham of Hallyards, and the Sandilands family which followed a dubious property transaction.