He stayed not long here, for, having, before the general assembly held at Glasgow 1638, fully vindicated himself, both anent his affair with Dr. Cameron, while regent in the university, and his settlement in Ireland, he was, for his great parts and known abilities, by them ordered to be transported to St. Andrews; but the assembly's motives to this did prove his determent for some time, and the burgh of Ayr, where the Lord had begun to bless his labours, had the favour for another year. But the assembly held at Edinburgh 1630, being offended for his disobeying, ordered him peremptorily to transport himself thither.
Anno 1640, when the king had, by the advice of the clergy, caused burn the articles of the former treaty with the Scots, and again prepared to chastise them with a royal army, the Scots, resolving not always to play after-game, raised an army, invaded England, routed about 4000 English at Newburn, had Newcastle surrendered to them, and within two days, were masters of Durham; which produced a new treaty, more favourable to them than the former; and with this army was Mr. Blair, who went with lord Lindsay's regiment; and, when that treaty was on foot, the committee of estates and the army sent him up to assist the commissioners with his best advice.
Again after the rebellion in Ireland 1641, those who survived the storm, supplicated the general assembly 1642, for a supply of ministers, when severals went over, and among the first Mr. Blair. During his stay there, he generally preached once every day, and twice on Sabbath, and frequently in the field, the auditors being so large, and in some of these he administered the Lord's supper.
After his return, the condition of the church and state was various during the years 1643, and 1644; and particularly in Aug. 1643, the committee of the general assembly, whereof Mr. Blair was one, with John earl of Rutland, and other Scots commissioners from the parliament of England, and Messrs. Stephen Marshal and Philip Nye, ministers, agreed to a solemn league and covenant betwixt the two kingdoms of Scotland and England; and in the end of the same year, when the Scots assisted the English parliament, Mr. Blair was, by the commission of the general assembly, appointed minister to the earl of Crawford's regiment; with whom he stayed until the king was routed at Marston-muir July 1644, when he returned to his charge at St. Andrews.
The parliament and commission of the kirk sat at Perth in July 1645. The parliament was opened with a sermon by Mr. Blair; and, after he had, upon the forenoon of the 27th, a day of solemn humiliation preached again to the parliament, he rode out to the army, then encamped at Torgondermy, and preached to Crawford's and Maitland's regiments, to the first of whom he had been chaplain:—He told the brigade, That he was informed that many of them were turned dissolute and profane, and assured them, that though the Lord had covered their heads in the day of battle (few of them being killed at Marston-muir), they should not be able to stand before a less formidable foe, unless they repented. Though this freedom was taken in good part from one who wished them well, yet was too little laid to heart; and the most part of Crawford's regiment were cut off at Kilsyth in three weeks afterwards.
After the defeat at Kilsyth, severals were for treating with Montrose, but Mr. Blair opposed it, so that nothing was concluded until the Lord began to look upon the affliction of his people; for the committee of estates recalled general Leslie, with 4000 foot and 1000 dragoons, from England, to oppose whom Montrose marched southward; but was shamefully defeated at Philiphaugh Sept. 13, many of his forces being killed and taken prisoners, and he hardly escaped. On the 26, the parliament and commission of the general assembly sat down at St. Andrews (the plague being then in Edinburgh); here Mr. Blair preached before the parliament, and also prayed before the several sessions thereof; and when several prisoners, taken at Philiphaugh, were tried, three of them, viz. Sir Robert Spotiswood, Nathaniel Gordon, and Mr. Andrew Guthrie, were to be executed on the 17th of January thereafter, Mr. Blair visited them often, and was at much pains with them: He prevailed so far with Gordon, that he desired to be relaxed from the sentence of excommunication which he was under; and accordingly Mr. Blair did the same: The other two, who were bishops sons, died impenitent.—Mali corvi malum ovum.
Anno 1646, the general assembly, sitting at Edinburgh ordered Mr. Blair (who was then moderator), with Mr. Cant and Mr. Robert Douglas, to repair to the king at Newcastle, to concur with worthy Mr. Alexander Henderson and others, who were labouring to convince him great bloodshed in these kingdoms, and reconcile him to presbyterian church-government and the covenants. When these three ministers got a hearing, the room was immediately filled with several sorts of people to see their reception; Mr. Andrew Cant, bring eldest, began briskly to insinuate, with his wonted zeal and plainness, that the king favoured popery; Mr. Blair interrupted him, and modestly hinted, That it was not a fit time nor place for that.—The king, looking on him earnestly, said, "That honest man speaks wisely and discreetly; therefore I appoint you three to attend me to-morrow at ten o'clock in my bed-chamber." They attended, according to appointment, but got little satisfaction; only Mr. Blair asked his majesty, If there were not abominations in popery, &c. The king, lifting his hat, said, "I take God to witness that there are abominations in popery, which I so much abhor, that ere I consent to them, I would rather lose my life and crown." Yet after all this, Mr. Blair and Mr. Henderson (for these two he favoured most) having most earnestly desired him to satisfy the just desires of his subjects, he obstinately refused, though they besought it on their knees with tears. Renewed commissions for this end, were sent from Scotland, but to no good purpose, and Mr. Blair returned home to St. Andrews.
Mr. Henderson died at Edinburgh, Aug. 19, which the king no sooner heard, than he sent for Mr. Blair to supply his place, as chaplain in Scotland; which Mr. Blair, thro' fear of being insnared, was at first averse unto, but having consulted with Mr. David Dickson, and reflecting that Mr. Henderson had held his integrity fast unto the end, he applied himself to that employment with great diligence, every day praying before dinner and supper in the presence chamber; on the Lord's day lecturing once and preaching twice; besides preaching some week days in St. Nicholas's church; as also conversing much with the king, desiring him to condescend to the just desires of his parliament, and at other times debating concerning prelacy, liturgies and ceremonies.
One day after prayer, the king asked him, If it was warrantable in prayer to determine a controversy?—Mr. Blair, taking the hint, said, He thought he had determined no controversy in that prayer. Yes, said the king, you have determined the pope to be antichrist, which is a controversy among orthodox divines. To this Mr. Blair replied, To me this is no controversy, and I am sorry it should be accounted so by your majesty, sure it was none to your father. This silenced the king, for he was a great defender of his father's opinions; and his testimony, Mr. Blair knew well, was of more authority with him than the testimony of any divine. After a few months stay, Mr. Blair was permitted to visit his flock and family.
After the sitting of the Scots parliament, Mr. Blair made another visit to the king at Newcastle, where he urged him with all the arguments he was master of, to subscribe the covenants, and abolish Episcopacy in England, and he was confident all his honest Scotsmen would espouse his quarrel against his enemies in England, &c. To which the king answered, That he was bound by his great oath to defend Episcopacy, &c. in that church, and ere he wronged his conscience by violating his coronation-oath, he would lose his crown. Mr. Blair asked the form of that oath; he said, It was to maintain it to the utmost of his power.—Then, said Mr. Blair, you have not only defended it to the utmost of your power, but so long and so far, that now you have no power, &c. But by nothing could he prevail upon the king, and left him with a sorrowful heart, and returned to St. Andrews.