1500-1520
Scotland and France were allies, upon an agreement called the “Auld Alliance.” This began in 1295, and ended in July 1560. The two countries were an enemy against England, with plenty of warfare.
In 1503, King James IV of Scotland married Margaret Tudor, establishing a dynastic link between the two countries
When James IV died via the hands of the English at Flodden in 1513, he was succeeded by James V - an infant at the time. 

1520-1540
Somewhere towards the early 1520s, both manuscript and printed versions of Martin Luther’s reform ideas were published and spread widely around Scotland. Primarily being shared around the east coast ports by merchants and trade vessels from the “Low Countries” - modernly The Netherlands, Belgium, Luxembourg, also known as Benelux - and Baltic states - Estonia, Latvia, Lithuania. 
Due to these versions of the reform ideas being so available, laws were put in place to outlaw their spread in 1525. These were known as ‘Act anent heresy’ which banned their importation and reading, the punishment being loss of property and goods.
A little later, in 1527, a student and university master known as Patrick Hamilton returned to St Andrews, from Germany. He’d go on to become the first Protestant martyr killed for spreading the message of reform, having returned and started to endorse Lutheran beliefs. Patrick Hamilton was burned outside the gates of St Salvator’s university in 1528.
Between 1528-1532 there were numerous cases of Catholic churches being desecrated, martyrdoms for heresy in St Andrews in 1538-9, and a small group of people being killed for Protestant beliefs in 1943.
At this point, Protestantism wasn’t very widespread at all. 
1540-1549
The first Scot to return with the Swiss reform message, instead of the German reform message, being preached at the time was George Wishart. Wishart began to preach somewhere circa 1545, and he was later put to death in March 1546 on a trial presided by Cardinal David Beaton. This somehow managed to make his message stronger, as Wishart willingly let himself be burnt alive - going as far as to kiss and embrace his executioner out of forgiveness. John Knox was inspired by him, as well as a few others. 
After King James V died in 1542, Queen Mary became the new monarch - still an infant at the time. This blank period allowed those interested in Protestantism space to explore those ideas without risk of punishment. 
Also around this time, Protestantism began to mix with positive feelings toward England, a country that had already withdrawn from Catholicism due to Henry VIII somewhere around the 1530s.
A regency council consisting of Cardinal David Beaton, James Hamilton earl of Arran, as well as the earls of Moray, Argyll, and Huntly was decided in late 1542. Though less than a year later Arran had Beaton imprisoned and took control, writing to Henry VIII and promising reformation.
After taking over in power, Arran authorised people to read vernacular bibles which became very popular to spread the word of Protestantism. 
During this, many Anglo-Scottish “assured lords” arranged a peace treaty between Scotland and England, known as the Treaties of Greenwich. This would entail marrying Queen Mary to Henry VIII’s heir, Prince Edward. This plan was agreed to by Arran.
Soon after, in late 1543, Arran lost power because of a counter-coup by Beaton - who quickly renounced the treaties. Though, at that point Protestantism had already been briefly legitimated by the government.
Beaton later went on to be murdered by Protestants in 1546. John Hamilton thereafter took his place, however it was 2 years before he was given the authority to act as the Archbishop of St Andrews
After the Battle of Pinkie in 1547, English garrisons along the border handed out bibles written in English. 
Around this time, Queen Mary was betrothed and sent to France at the age of 6. 


1550-1559
Although there was a growing population of Protestants, if French influence returned it was possible that Catholicism would overtake it and be restored as Scotland’s primary religion. Parts of this showed through exiles led by John Knox and Christopher Goodman. These exiles were greatly helped when England returned to being a Catholic state during Mary Tudor’s rule during 1553 as this left Protestants with no place on the British mainland. 
Mary of Guise, Queen Mary’s mother, was made regent of Scotland in 1554. She was regarded as an effective ruler, rewarding those who were loyal with money and land, and bribing the people that may stray.
Mary of Guise attempted to restore a firm central government and deal with administering justice and regulating trade but Scottish nobles grew suspicious of her.
In 1556 there was an effort made to enact a form of valuation tax, though this led to the Scottish nobility losing trust in her. 
Later, Mary attempted to engineer war against England in October 1557, but the principal Scots noblemen refused to fight at the Borders. Scottish Lords came together to promote Protestantism, and were known as the Lords of the Congregation. 
The Lords of the Congregation did not like Mary of Guise and what she was doing. They desired change in the Church.
Despite how powerful of a ruler Mary of Guise was, she made little attempt to counter religious reform. Due to the previous murder of Beaton, there was nobody to fill the gap while John Hamilton assumed his place. This absence of leadership allowed for Protestantism to silently spread; meetings were held with secrecy, even the more public meetings were still closed off. 
In 1558 within East Coast burghs, Protestants began gathering to worship using the English Prayer Book. The fact that Elizabeth became the Protestant Queen of England around that time benefited their cause greatly, motivating them to keep spreading their words.


1559
At the beginning of 1559 there was a notice placed on doors of monasteries, friaries, and abbeys, it threatened dispossession of friars. This letter was known as “The Beggars’ Summons” and it was addressed from the “blind, crooked, bed-ridden, widows, orphans, and poor of Scotland.” Additionally, Perth and Dundee announced they were now Protestant towns.
John Knox arrived in Leith on the 2nd of May 1559, giving the protestant cause a boost in direction. Knox preached in St John’s Kirk, though his sermons caused outrage which led people to destroy religious property and decorations. When the Protestants took over Stirling and Edinburgh, Knox became the minister of St Giles. 
2,500 men under the earl of Glencairn prepared for defence in Perth against Mary of Guise. Eventually, Glencairn’s men gave Perth to Guise, and she instantly pushed for Catholicism through martial law. This was, unsurprisingly, very disliked - especially as her troops shot a boy dead during reoccupation. 
This chain of events led Lord James Stewart and the earl of Argyll to become leaders of the “Lords of the Congregation.” They went on to ‘reform’ St Andrews and Edinburgh by ransacking their way through. 

1560
In June of 1560, Mary of Guise died. This left Scotland without royal sanction, and so the Lords of the Congregation were quick to invite in the new age of religious reform.
In July of 1560 a treaty known as the “Treaty of Edinburgh” was signed. This replaced the Auld Alliance, and led to France and England to leave Scotland to handle itself for the time being.
The Lords of Congregation secured power in August. This revolution would change Scotland forever, its church, its culture, its history. 
The meeting held was known as the Reformation Parliament, it outlawed Catholic worship and rejected the notion of the Pope having any authority over Scotland. It also outlawed Catholic mass as a whole. 
A group of Protestants created a polity “touching the reform of religion in Scotland”. This was the concept for what would later develop into the Kirk of Scotland, and was known as the First Book of Discipline. It posited John Knox’s ideal, but drastic, changes, such as:
The new Protestant Church gaining the properties of the Catholic Church.
Superintendents, without specific religious powers, organising the church in their areas.
Congregations playing a key role in the new Church by appointing their ministers.
The Protestant Church providing education and looking after the poor.
Though these ideas weren’t very well liked, and this book was rejected. They did however strip previously Catholic churches of religious art involving idols.

1561-1570
Upon Mary Queen of Scots’ abdication, James became king despite being an infant. 
This began a set of Regents, the first being Mary’s half brother, the Earl of Moray. Moray had to deal with Mary still having heavy support throughout Scotland.
Moray garnered Protestant support via the passing of laws of the Reformation Parliament of 1560, these favoured the Kirk. Additionally, he took action against Catholic priests, and this pleased the Protestants.
Moray was later murdered in Linlithgow by one of Mary’s supporters. 
Moray’s successor was the Earl of Lennox, and then the Earl of Mar. 


1570-1578
In 1572 the Earl of Morton stepped up to be regent, and his job was to guide policy until James became an adult. He tried to restore law & order, as well as secure Protestantism.
It was put upon town councillors and ministers to declare they accepted loyalty to the King and the Kirk. Bishops were appointed as well.
When Andrew Melville arrived back in Scotland after spending a decade away both studying and teaching in France, he was appointed the position of Principal - first of the University of Glasgow, and then St Andrews University. 
The new leader of the Reformed Church in Scotland was supposed to be Melville, though he held differing opinions than Knox. For example, he wanted a theocracy, and he was opposed to bishops. He desired no hierarchy, and he wished for the church to have a self sufficient organisation, separate from the King and Parliament, using presbyteries and general assemblies. Such a concept would mean the Kirk would be in charge of the church as opposed to the King.
Soon after this, Morton grew to be resented by the nobles and later executed (in 1581) for accused of complicity in the murder of Lord Darnley. 


1578-1584
As of 1581 the Church had plans in place for 13 Presbyteries, which would give them power like appointment of ministers, discipline, and representatives attendance for the General Assembly. This meant that the Kirk could function independently, and decisions at a parish level were made by elders and deacons known as the Kirk Session. 
Kirk Sessions were to set standards, fine people, and stress the need to attend both daily and Sunday services. All of these rules allowed the Kirk authority over members in the congregation. 
In 1582, James VI was kidnapped by Presbyterians who were trying to gain control over the government. These people, who were known as the Presbyterian Lords, were led by William Ruthven. Ruthven had temporary control over Scotland, for 10 months. This set of events is known as the Ruthven Raid.
James VI managed to escape in 1583, and assumed control of Scotland himself at the direction of the Earl of Arran. 
After the first Book of Discipline was rejected by Melville, this time outlining Melville’s ideas that the Kirk is to receive authority from God instead of the state. It also directly stated his opposition to bishops. It went as far to suggest an organisation where bishops were excluded and their duties were instead taken by ministers and elders, known as the Presbytery. Many meetings followed this so they could figure out religious teaching.
In 1584, after the Ruthven Raid had demonstrated their threat level, King James convinced Parliament to pass the “Black Acts”, these included:
No minister would in future be exempt from the judgement of the ordinary courts.
Anyone who criticised the King, even from the pulpit, would be punished.
No church court could sit in judgement except with the consent of the King.
Royal supremacy over the Kirk was clearly established.

Summary