November 1559 - July 1560.
Inevitably the Act of Separation and letter to the Regent Mary informing her of the decision hardened attitudes. First to enter the lists was the Congregation who by sound of trumpet and declaration sought the French troops and foreign Scots ( also soldiers in the main) in Leith to leave the town; and residents were asked to stop the fortification work. This almost naive, playing by the rules, action achieved nothing save disregard and some minor skirmishing. It was perhaps indicative of the amateur way the Congregation`s affairs were conducted in the following months.
There followed several weeks of setbacks for the Congregation as their cause wavered without clear direction or action. Regent Mary continued to try to divide and rule, and in time people began to slip away while spies, some say traitors, kept Mary informed. The wavering James Hamilton, Duke of Chatelherault was subject of pressures and suggestions that he had become a supporter of the Congregation (which he had). The soldiers of the Congregation were desperate for pay and their leaders who had anything left gave up their silverware to be coined to pay them. Lord James is said to have paid out over 13,000 crowns of his own money since the 10th of May when his force was assembled. Meanwhile 4000 crowns, from Sir Rawfe Sadler and Sir James Crofts at Berwick, was seized by the Earl of Bothwell and never recovered despite hot pursuit by Argyll, Lord James and the Master of Maxwell. At almost the same time a foray by a Dundee contingent of the Congregation forces sought to fire their cannon on the French in Leith, but this failed because of deserting soldiers and a French initiative to charge and seize the cannons. An assault by the French on 5 November almost succeeded in which some thirty men died and some gentlemen were captured. On the other hand they gained the support of William Maitland of Lethington, the younger - a secretary to the Regent, who confirmed that there was "nothing but craft and falsehood in the queene." Amid much wailing, the decision was taken that the Congregation should leave Edinburgh and reconvene at Stirling .
Knox preached on 7 November at Stirling and fairly roasted the Congregation for their indecision and lack of resolve. The telling off put some spirit back into the Congregation who that evening met and appointed Robert Melvill and William Maitland to go to Queen Elizabeth in England and make known their position. Meanwhile, the Lords and their forces divided into two groups, Argyll, Glencairn and Maxwell in Glasgow and Lord James and the Earl of Arran in Fife, each to give support to the people there.
Following on the departure from Edinburgh, the houses of the burgesses were given to Frenchmen as a reward, and Bothwell appeared from hiding to declare the Earl of Arran a traitor. Hearing that the Congregation were reconvening in Stirling [ to provide answers to questions from the English Court ] the French set out to take them. On the way they ransacked Linlithgow, the Duke of Chatelherault`s home, and wasted the lands of Kinneill. This prompted Argyll and Glencairn and friends to go to Glasgow while Lord James and the Earl of Arran went to Saint Andrews then to Cupar. The French now turned their attention to Fife, intending to fortify the town, castle and Abbey of St Andrews. On the way they started to fortify Burntisland, while Lord James sent soldiers to Kinghorn but it was taken by the French. In Fife at this time the French had about 4,000 soldiers while the Congregation`s forces amounted to some five hundred horsemen and one hundred soldiers. Now centered at Dysart, the Congregation`s forces continued to skirmish daily for over three weeks during which Lord James and Arran slept clothed and with boots on the whole time.
A new dimension to the conflict was the need for the French to service their troops in Fife. Two of their vessels were seized by ships sent from Dundee, prompting a French vow to take St Andrews and Dundee. To this end they contracted a Captain Cullane and two ships to ferry supplies to Kinghorn. A real turning point in the conflict then emerged when on Monday 23 January 1560, English ships appeared in the Forth and took Captain Cullane and his ships prisoner. The word to the French commanders was that these English ships were the first of many more to come. The `excuse` offered by the English was that the warships were seeking pirates who were active along the coasts. As Knox wrote in a letter, the French " retired more in one day than they advanced in two". In their withdrawal back to Leith there was much pillaging and wasting of both Papist and Protestant property by the French troops. The tale is told of a Frenchman in a red cloak who took bread from an old woman in Stirling, then sought to take a little salt beef and meal she had for her children. When the soldier bent over the meal chest (kiste) she tipped his heels up, so that he fell into the chest and was suffocated.
The negotiations in England meanwhile, were bearing fruit as evidenced by the happy arrival of the English warships in the Forth. Elizabeth despatched the Duke of Norfolk to the North of England to determine what the Scots needs were. When the Congregation were approached about a meeting place, Maxwell said Carlisle - seemingly for his own convenience to his estates in Dumfriesshire. This would have meant the likes of Lord James having to travel, at considerable personal risk, from St Andrews. This prompted Knox to write to the Lords in Glasgow on 6 February whence he castigated them for their relative inactivity and lack of consideration for those who had been fighting their cause. Shaking off their lethargy it was agreed to meet with the Duke of Norfolk at Berwick. On 27 February the parties met, the nature of assistance to the Scots agreed, and the Treaty of Berwick signed.
The French response was to lay waste much of the Lothians and the surrounds of Glasgow leaving little that might be of use to an English army. This duly crossed the border on April 2nd, under the command of Lord Scroope, numbering 6,000 foot and 2,000 horse. Meanwhile the Congregation had accepted the Earl of Huntly into their ranks thus removing the risk of intervention from the north. The Regent, Mary, sought the protection of Edinburgh Castle. On Palm Sunday, 6 April the French and English forces began skirmishing at Leith with some losses on both sides. On April 15th a larger force of Frenchmen - fifty horse and about 500 harquebusiers (riflemen) attacked. They were eventually repulsed after they had managed to `stop` the fire holes of some cannon. This resulted in a reordering of the battle plans and the building
of mounts at strategic points for their cannon, thereby tightening the English grip on Leith. As was their wont, the Congregation convened and subscribed a Band of mutual cooperation at Edinburgh on 27 April.
In Edinburgh Castle the Regent Mary was distraught when she read the Band and complained bitterly at the bad advice she had received from all and sundry.
" The malidiction of God light on them who counselled me to persecute the preachers, and to refuse the petitions of the best part of the true subjects of this realme !"
To rub salt in to her wounds the wasting of the surrounds of Leith to create shortage of victuals for the English troops was to no avail, as the people produced hidden stores and accepted lower prices, such was their distaste for the French.
At Leith the assault trenches were taken as far as they could be by the English and on 7 May began an attack that lasted some ten hours. At one point they had secured an entry but the scaling ladders were just too short to enable the soldiers to reinforce those on the top of the walls. There was strong suspicion that someone, possibly Sir James Crofts, whose own soldiers did not take part, was responsible. In the event the assault failed and the French claimed a short lived victory. At this point the French were observed stripping the dead naked and leaving the bodies exposed for several days. At this the Regent crowed (in tones not dissimilar to those attributed to Cardinal Beaton at the execution of George Wishart) "Yonder the fairest tapestrie that I ever saw. I would the whole field betwixt me and them were strowed with the same stuffe." Despite the setback, the Duke of Norfolk ordered the siege to continue and sent 2000 fresh troops and a promise of more if needed.
The final twist in the drama soon followed when a letter from the Regent to Msr D`Oysell was intercepted in which she sought some medication for herself although there was apparently a secret message within. The letter was destroyed . Subsequently she sought to speak to Argyll and Glencairn and others, but they suspected a trap and saw her one at a time during which meetings she expressed regrets at the war. On 9 or 10 June Mary of Guise died " consumed partlie with grievous displeasure and melacholie, partlie with longsome and incurable sickness." Her body was encased in lead and lay in Edinburgh Castle until 19 October before it was shipped to France for burial.
Before the Regent`s death the king of France had despatched ambassadors to England to treat for peace with Elizabeth ( He refused to deal with the Scots whom he viewed as his subjects - which they were by marriage). The ambassadors` work continued in the new circumstances and a peace was agreed in July. The French soldiers were transported to France, mainly by English ships, and the English soldiers returned over the border on 16 July. Suddenly, almost against the odds, it was all over leaving the Congregation in charge, a parliament to be convened, and a Protestant Church to be ratified. The Confession of Faith was produced in a very short time and ratified by the Estates of Parliament on 17 August 1560 along with Acts abolishing the jurisdiction of the Pope and the saying of the Mass.
But the Reformation was to take a further 130 years before the Presbyterian Church was finally established in Scotland.