Pro-French policy
Regent Arran celebrated the Treaty of Greenwich at the Holyrood Abbey on 25 August 1543. However, in September Arran turned around. He secretly met Cardinal Beaton at Callendar House and reconciled himself with his former enemy. Shortly after he became Catholic and joined the pro-French faction. Around this time Friar Mark Hamilton wrote a history of the Hamilton family. Arran made penance for his "godly fit" at the Franciscan Friary in Stirling. Mary, Queen of Scots, was crowned at Stirling on 9 September.
Arran captured Dalkeith Castle in November 1543, but failed to capture the pro-English George Douglas. In December, the Parliament of Scotland declared the Treaty of Greenwich void due to shipping incidents. The seven-year war with England now called the Rough Wooing was declared on 20 December 1543. Arran spent Christmas with Mary of Guise at Stirling Castle where they played cards. The declaration of war was brought by Henry Ray to give to Parliament. Arran replied that the parliament was dissolved, and so he thought it expedient not to answer Henry VIII on the points raised at the time.
In 1544 an attempt was made to transfer the regency from him to Mary of Guise. A convention or Parliament of the nobility at Stirling in June suggested she should be regent instead. Conflict seemed possible, but Arran when fortified Edinburgh her forces retired. Arran held a Parliament in November 1544 and declare the resolutions of the June meeting to be of no effect. Later, in March 1545, he agreed to abandon some of his responsibilities to her and she formed an advisory council. Arran and Cardinal Beaton decided to act against the Earl of Lennox and besieged Glasgow Castle in March 1544.
In June 1547 Arran gathered a large army to expel the English from Langholm and the surrounding area. He had a banner made from taffeta decorated with gold foil and colours, and another banner for his trumpeter. Horses dragged the artillery and carts laden with cannonballs and tents out of Edinburgh Castle. The guns were dragged toward Langholm with oxen. Arran had an armoured "jack" covered with purple taffeta, then changed his mind, choosing purple velvet. A Scottish spy, David Maitland, who signed himself "Ye Wait Quha" wrote of the preparations to Thomas Wharton, that it was "the starkest host and the monest, and with the best order that wes sen Flodwn", that is, "the strongest host and most numerous, in the best order since Flodden."
Edward Seymour, Duke of Somerset sent tracts into Scotland, hoping to garner support for the English cause. His agents were ordered to display his proclamation on church doors and even on the gate of Stirling Castle. On 25 August 1547, Arran gave orders that no one should read the proclamations "set forth in print in Scotland to seduce the hearts of the people to his opinion".
In September 1547, Arran assembled a large Scottish army to resist an English invasion led by the Duke of Somerset but was defeated at the battle of Pinkie. He was forced to abandon some of his clothes at the battlefield.
Arran nevertheless held onto the regency and continued to lead forces against the occupying troops. For two weeks in February 1548, he led a campaign in Teviotdale with Monsieur d'Essé to recapture Ferniehirst Castle and punish borderers. He held discussions at Jedburgh with Nicolas Durand de Villegaignon over the site and financing of a new fort.
Arran reluctantly agreed in July 1548 to Mary's marriage to Francis, eldest son of Henry II of France. Mary was sent to France. Henry II, by the Treaty of Haddington claimed to be Protector of Scotland, and rewarded Arran by making him Duke of Châtellerault on 8 February 1549 and a knight of the Order of Saint Michael.
On 19 April 1550, Regent Arran and his Privy Council made legislation about foodstuffs and rising prices. The people of Scotland were to reduce their diets and banqueting. Prices were set for wild birds and rabbits, swans would be 5 shillings, plovers 5 pence. River birds including herons and ducks were to be caught by hawking. It was forbidden to shoot deer or birds for the table with "half hag or culverin or pistolate". These acts were ratified by Parliament.
Arran came to the north of Scotland in 1552, visiting Aberdeen, Dunnotar Castle, and Huntly Castle where his daughter Barbara Hamilton lived with the family of her husband Alexander, Lord Gordon. He held "justice ayres" or courts and was accompanied by musicians, much like a Scottish monarch on progress.