Mary in Scotland
During the personal reign of Mary in Scotland George had a loyal inscription set in large carved letters and gilded above the entrance to Seton Palace;"UN DIEU, UN FOY, UN ROY, UN LOY"One God for all time: One loyalty to the monarch. Lord Seton had dies made by the Edinburgh goldsmith Michael Gilbert to strike gold and silver medals with the same motto, and a monogram with his initials and those of his wife, Isobel Hamilton, "GS-IH," with another motto "Nemo Potest Duobus Dominus Servire," from Matthew 6:24, "No one can serve two masters."
Mary was unsuccessful in proposing Seton as Provost of Edinburgh again in October 1561. Next year she made a better choice by backing Archibald Douglas (II) of Kilspindie, now associated with the success of the Reformation.
In March 1565, Seton fought a duel with Francis Douglas who was badly injured. The Earl of Morton and the Laird of Lethington tried to take legal action so Seton went to France. Thomas Randolph, the English diplomat, heard that Mary and Lord Darnley went to Seton Palace and were "bedded" after their marriage at Holyroodhouse. Seton returned to Scotland in October 1565, during the Chaseabout Raid. He carried arms from France for Queen Mary. An English ship, the Aid tried to blockade Leith to prevent him docking, but was repulsed. Seton's cargo included three great horses for Darnley.
The French ambassador, Jean, Count de Brienne, arrived in Edinburgh on 2 November 1566 and was lodged in Henry Kinloch's house in the Canongate near Holyrood Palace. He went to Stirling Castle for the baptism of Prince James on 12 December, escorted by Lord Seton.
Days after the death of Lord Darnley, on 17 February 1567, Mary had a blue costume for her fool called George Steven delivered to her at Seton Palace, in April she was there with her council. With other supporters of Mary's marriage to James Hepburn, 4th Earl of Bothwell Seton signed the Ainslie Tavern Bond on 19 April 1567.
Mary's marriage to Bothwell and continued rule in Scotland was opposed by the Confederate Lords. She stayed at Seton Palace before her capture nearby at the battle of Carberry Hill. She was then imprisoned at Lochleven Castle. She escaped to Seton's castle at Niddry but her supporters were defeated again at the battle of Langside. Seton was taken prisoner and early reports thought him killed. The son of Lord Ochiltree, John Knox's brother-in-law, would have killed him in revenge for his father's injury, but he yielded and was saved by James Stewart, 1st Earl of Moray.
Queen Mary went into England, where her companion, Seton's half-sister Mary Seton joined her. With the other Marian lords Seton was imprisoned in Edinburgh Castle where Mary was worried that he was at risk from plague. Seton was finally allowed to go into exile in France. Elizabeth I of England sent him a passport on 1 June 1569.