Following the extensive reforms enacted at the 1638 Glasgow General Assembly in contravention of Charles I's command, war loomed between Scotland and England, but Robert Baillie hesitated to countenance armed resistance. Whilst Covenanters such as Samuel Rutherford voiced their support for war, Baillie was unsure whether Charles's alterations of the Scottish Church's doctrine and liturgy warranted such dramatic measures. After agonizing over the lawfulness of defensive arms, in February 1639 Baillie ultimately acquiesced, explaining to his cousin William Spang that he did not determine that resistance was lawful from reading ‘[David] Paraeus or Buchanan, or Junius Brutus, for their reasons and conclusions I yet scunner [i.e. shudder] at; bot mainly by Bilsone de Subjectione, where he defends the practise of all Europe … who at diverse tymes, for sundry causes, hes opposed their princes’. Baillie had become convinced of the lawfulness of defensive arms from reading The True Difference betweene Christian Subjection and Unchristian rebellion (1585) by the Elizabethan bishop Thomas Bilson, hardly an author commonly included in the canon of resistance theorists. On the one hand, Bilson had defended a robust conception of hereditary monarchy, arguing that religion could not justify rebellion. On the other hand, he asserted that subjects must resist a monarch when they cease to act in line with God's laws: Protestants may justly raise arms against their monarch if they reintroduced Roman Catholic beliefs into a national church.

Baillie's ideas concerning the foundation and limits of monarchical power distinguished him from his compatriot Rutherford, traditionally considered the main political theorist of the Covenanting movement. Baillie's political thought also challenges historiographical consensus that Covenanting political thought was predominantly influenced by late sixteenth-century ‘monarchomach’ authors such as George Buchanan, John Knox and ‘Junius Brutus’ – the anonymous author of Vindiciae contra tyrannos (1579). Whilst the influence of Buchanan's historical tract Rerum Scoticarum Historia (1582) remained pervasive on seventeenth-century Scottish intellectual culture, the influence of Buchanan's writings on resistance theory are more difficult to ascertain.