Soon after the National Covenant was signed, king Charles I   had begun preparing for war against the Covenanters. He was determined to regain his control over the Scottish Church. By July 1638, both sides had been openly arming for war. Charles spent the rest of 1638 playing for time until his army was ready. The actions of the General Assembly in Glasgow in November had made war even more certain. The Covenanters now got Alexander Henderson to write in defence of their resisting the king, but still tried peaceful alternatives such as appealing to the English Parliament.

The first battles were in February 1639 and by March the Covenanters had captured Edinburgh castle without firing a shot, after blowing up the outer gate. Few in England were keen on a war with Scotland and the king struggled to gather a big enough army. The Covenanters also struggled to gather an army that was well-supplied or trained, but those they did round up were enthusiastic about the cause. By June, the Covenanters had forced the king to agree to the Treaty of Berwick. As part of the treaty, the king agreed to allow a free General Assembly. All future religious matters would be decided by church assemblies, and civil matters by parliament

Read more:
BCW: Bishops’ Wars
David Stevenson, The Scottish Revolution, 1637-44 (2nd edn, Edinburgh, 2003), pp 127-61.
DSCHT: Bishops’ Wars
Mark A. Kishlansky and John Morrill, ‘Charles I (1600–1649)’, Oxford Dictionary of National Biography, Oxford University Press, Sept 2004; online edn, Oct 2008