The Scots Covenanters had taken the side of the English Parliament during the English Civil War and had fought a bitter Wars of the Three Kingdoms at home against the Scottish Royalists. However, they were excluded from negotiations by the victorious English Parliament and by 1647, they despaired of achieving their political goals - the establishment of Presbyterianism in the Three Kingdoms and asserting the civil authority of the Scots Parliament and the General Assembly of the Scottish Kirk (Presbyterian Church). They even suspected that the Parliamentarians would annex Scotland and impose their own "Independent" religious settlement. For this reason, one faction of the Covenanters, the Engagers, signed a secret deal with Charles I called the "Engagement". However, they were defeated in an attempted invasion of England and even came to blows with fellow Covenanters who wanted a more forthright deal with the King.
When Charles I was executed in 1649, the radical Covenanters, or "Kirk Party", moved to do a new deal with Charles II, the son of the dead King, who was in exile in Breda. The treaty basically granted everything the Kirk Party wanted. Charles II undertook to establish Presbyterianism as the national religion and to recognise the authority of the Kirk's General Assembly in civil law in England as it already was in Scotland. Charles also took the Solemn League and Covenant oath of 1643.
Charles was crowned King of Scots in Scone in January 1651, but by then the terms agreed at Breda were already a dead letter. The army associated with the Kirk Party under David Leslie was destroyed by Oliver Cromwell at the Battle of Dunbar in September 1650 and the English Parliamentarian New Model Army had taken Edinburgh and much of Lowland Scotland. Even a subsequent rapprochement between moderate and radical Covenanters and their former enemies, the Scottish Royalists, was not enough to restore Charles' throne. He fled the country for France after his defeat at the battle of Worcester in September 1651.
Under the Commonwealth of England, Scotland was annexed, its legislative institutions abolished and Presbyterianism dis-established. There was freedom of religion under the Commonwealth, except for Roman Catholics, but the edicts of the Kirk's assemblies were no longer enforced by law, as previously.
After being restored to his throne in 1660 King Charles completely reneged on the Treaty of Breda, seeking to restore an Episcopalian church structure in Scotland.