James VI was born into the intrigues of Scotland's late 16th century political and religious world. He was born six years after the Scottish Reformation had overturned the Catholic hierarchical system of religious worship. Following the lead of reformers in Europe, such as Martin Luther, people like the martyred George Wishart and latterly John Knox challenged what they saw as a corrupt church.

James's mother Mary, Queen of Scots, was a Catholic queen newly returned from France who had attempted to govern in this far from welcoming country. She was unable to convince the reformer John Knox that her motives were not to overturn the aims of the Reformation, and he proved a remorseless campaigner against her rule and her practised religion.

Edinburgh Castle was already an important royal fortress by Queen Margaret's death there in 1093. It remained one of the key royal castles until it was largely replaced as a royal residence by the Palace of Holyrood in the early 16th century. Thereafter it became more a symbol of the power of royalty and a military fortress.

This painted decoration in the birthroom of James VI was added in 1617 in preparation for the king's 'hamecoming', his first visit to Scotland having become king of England in 1603. It consists of a large representation of the Royal Arms together with an inscription. The inscription reads: 'Lord Jesu Chryst that Crounit was with Thornse Preserve the Birth quhais Badgie heir is borne And send Hir Sonee Successione to Reigne still Lang in this Realme, if that it be Thy will Als grant O Lord quhat ever of Hir proseed Be to Thy Glorie Honer and Prais sobied.'

This is a picture of the shadow from the John Knox Statue in the courtyard of the Assembly Hall. He was an outstanding leader and preacher during the Scottish Reformation in the 1500s. He met with Mary, Queen of Scots on a few occasions but they could not reach a position of agreement, she believing her worshipping in private would be enough to minimise any difficulty, he believing it intolerable in a reformed Scotland. Knox preached at the coronation of James VI in 1567.

The reformation saw massive changes in the way religious worship was carried out. The protestant church became the dominant religion in Scotland, eventually leading to the establishment of the Church of Scotland. The General Assembly of the Church of Scotland is an annual event held in Edinburgh for a duration of a week always during the month of May. It is held at the Assembly Hall on The Mound. The General Assembly is the Kirk's Parliament, supreme court, and top tier of government. 1200 representatives known as 'commissioners,' gather from the Presbyteries to discuss important issues for the Church.

Mary, the only daughter of James V and his second wife, Mary of Guise, had ascended to the throne when she was six days old, but in 1548 was sent to France as the prospective bride of the French Dauphin, Francois, who she married in 1558. She returned to Scotland to resume control in 1561, after Francois's death. In 1565 she married her cousin, the Catholic nobleman Henry Stewart, Lord Darnley. Although Mary granted Darnley the title of king, his wish to secure the crown for himself and his heirs led him into a dispute with the Protestant party, led by Mary's half brother, James Stuart, Earl of Moray.

Darnley was involved in the murder in 1566 of Mary's Catholic private secretary, David Rizzio, who was deemed to have too much influence over the Queen. Darnley and Mary had one son, the future James VI and I, born in Edinburgh Castle, June 1566. Darnley, by then estranged from Mary, was himself murdered at Kirk o' Field in Edinburgh in February 1567 by the Queen's favourite, James Hepburn, 4th Earl of Bothwell. Bothwell and Mary were subsequently married in a Protestant ceremony in 1567. In June 1567 a coalition of the opposition, the 'Confederate Lords', successfully overcame Mary and Bothwell at Carberry Hill. She was imprisoned in Loch Leven Castle and forced to abdicate in favour of her son James. She subsequently escaped but, following defeat at Langside, fled to England in 1568 and her final captivity.