The Scottish Parliament had met in a Convention of Estates to state that Scottish people would act independently of the monarch.
The Claim of Right, drawn up by Scottish MPs at this Convention, declared that James had lost the throne through his actions.
The English Parliament however, had stated that James VII and II had abdicated. This suggested that, in Scotland, Parliament had more authority over the Crown than in England.
A Scottish Act of Settlement was passed in 1690 - this legalised a Presbyterian Scottish Kirk.
The Episcopalian Church, still strong in the North-east of Scotland, now supported the exiled James Stuart instead of William. This was because James would support an Episcopalian Church.
There was opposition to William in the Scottish Highlands and he placed stronger control over Highland clans.
On 13 February 1692, the Glencoe Massacre took place. William’s government troops killed 38 members of the MacDonald clan who had been late in recording their loyalty to the King.
The Scottish Parliament stated that the killings were an act of murder. The massacre worsened Anglo-Scottish relations and increased support for the Jacobites.
The Worcester Affair of 1705 created more tension between Scotland and King William.
The Worcester was an English ship, under the control of Captain Green. Its crew was captured by an angry mob when it went ashore at Leith, near Edinburgh and Green was executed for piracy, even though the evidence at his trial was unconvincing.
Scots continued to be suspicious of William’s advisors in Scotland. Many thought they were acting to prevent England being threatened by Scottish trade.
It was felt that as long as there was a joint monarchy - Scotland could never act independently of English control.