The first of his public appearances in the favours of that glorious work of reformation (commonly called the second reformation period) seems to have been about the beginning of 1638. When it came first to be known that Traquair was going up to the king, the deputies (afterward called the covenanters) were desirous that he would carry up an information, which the lord Balmerino and Mr. Johnston (the only advocates as yet trusted by the petitioners) had drawn up, and that he would present the same, with their supplication, to his majesty. But both these were rejected, and orders given by him to Traquair, to publish a proclamation at Edinburgh and Stirling, against the requisitions of the covenanters. Sixteen of the nobles, with many barons, gentlemen, burgesses, and ministers, did, after hearing said proclamation, cause Mr. Johnston read a protest against the same. And the same year, when the marquis of Hamilton caused publish another declaration, in name of the king, the covenanters, upon hearing it, gave in another protestation in the same place by Mr. Johnston; whereupon the earl of Cassils, in name of the nobility, Gibson of Durie, in name of the barons, Fletcher provost of Dundee, in name of the burgesses, Mr. Kerr minister at Preston, in name of the church, and Mr. Archibald Johnston, in name of all others, who adhered to the covenant, took instruments in the hands of three notaries, and, in all humility, offered a copy of the same to the herald at the cross of Edinburgh[124].

Upon the 9th of September, a declaration of the same nature being published, the noblemen, gentlemen, burgesses, &c. gave another protest, and Mr. Johnston header and advocate for the church, in name of all who adhered to the confession of faith, and covenant lately renewed within the kingdom, took instruments in the hands of three notaries there present, and offered a copy thereof to the herald at the cross of Edinburgh.

In the same year, when the famous general assembly sat down at Glasgow, in the month of November, Mr. Henderson, being chosen moderator, it was moved, That Mr. Johnston, who had hitherto served the tables at Edinburgh without reward, and yet with great diligence, skill and integrity, deserved the office of clerk above all others. After much reasoning, concerning him and some others (put on a leet for election), the rolls being called, on a vote for a clerk, it carried unanimously for Mr. Johnston, who then gave his oath for fidelity, diligence, and a conscientious use of the registers; and was admitted to all the rights, profits and privileges, which any in that office had formerly enjoyed; and instruments taken both of his admittance and acceptance.

Mr Johnston being thus installed, the moderator desired, that all who had any acts or books of former assemblies, would put them into his hands; whereupon Mr. Sandihills, (formerly clerk) exhibited two books, containing some acts from 1592, to that of Aberdeen in 1618, &c. and being interrogate concerning the rest, he solemnly averred, that he had received no more from the arch-bishop, and to his knowledge, he had no other belonging to the church. -- Then a farther motion was made by the assembly for recovering the rest, wanting, that if any had them, they should give them up, whereupon Mr. Johnston gave an evidence how deserving he was of the trust reposed in him, by producing on the table five books (being now seven in all), which were sufficient to make up a register of the church, from the beginning of the reformation; which was very acceptable to the whole assembly.

In the 24th session of this assembly, a commission was given to Mr. Johnston to be their procurator, and Mr. Dalgliesh to be their agent; and in their last session of December 20, an act passed, allowing him the instruction of all treaties and papers that concerned the church, prohibiting all printers from publishing any thing of that kind, not licensed by him.

But the king and the Canterburian faction, being highly displeased with the proceedings of this assembly, advanced with an army toward the borders, which made the covenanters, seeing the danger they were exposed unto, raise another army, with which, under the command of general Leslie, they marched towards the king's army, now encamped on the south side of Tweed, about three miles above Berwick. Upon their approach, the English began to faint, whereupon the king and the English nobility desired a treaty, which was easily granted by the Scots, who appointed the earls of Rothes, Dunfermline and Loudon, the sheriff of Teviotdale, Mr. Henderson and Mr. Archibald Johnston advocate for the church, as their commissioners to treat with the English commissioners, to whom his majesty granted a safe conduct upon the 9th of June, 1639. The Scots, having made known their demands, condescended upon several particulars, which were answered by the other side. On the 17th and the day following, the articles of specification were subscribed to by both parties, in sight of both armies at Birks near Berwick. But this treaty was but short lived, and as ill kept; for the very next year, the king took arms again against the Scots, who immediately armed themselves a second time, and went for England, where they defeated a party of the English at Newburn, and pushed their way as far as Durham. The king, finding himself in this strait, the English supplicating him behind, and the Scots with a potent army before him, resolved on a second treaty, which was set on foot at Rippon, and concluded at London; and thither Mr. Henderson and Mr. Johnston were sent again, as the commissioners for the church; in which affairs they behaved with great prudence and candor. When the Scots parliament sat down this year, they, by an act, appointed a fee of 100 merks to Mr. Johnston, as advocate for the church, and 500 merks as clerk to the general assembly; so sensible were they of his many services done to this church and nation.

Next year, 1641, the king, having fallen out with his English parliament, came to Scotland, where he attended the Scots parliament. In this parliament several offices of state were filled up with persons fit for such employments. The earl of Argyle being put at the head of the treasury, and the earl of Loudon made chancellor; among others, Mr. Archibald Johnston stood fair for the register office; and the generality of the well-affected thought it the just reward of his labours; but the king, Lennox and Argyle, &c. being for Gibson of Durie, he carried the prize. Yet Mr. Johnston's disappointment was supplied by the king's conferring the order of knight-hood upon him, and granting him a commission to be one of the lords of session, with an annual pension of 200 pounds; and Orbiston was made justice clerk[125].

During this and the next year Mr. (now Sir) Archibald Johnston had several great employments committed to his trust. He was one of those nominated to conserve the articles of peace betwixt the two kingdoms until the meeting of parliament, &c. And then he was appointed one of these commissioners, who were sent up to London to negotiate with the English parliament, for sending over some relief from Scotland to Ireland (it being then on the back of the Irish rebellion). While at London, they waited on his majesty at Windsor, and offered their mediation betwixt him and his two houses of parliament; but for this he gave them little thanks, although he found his mistake afterwards.

When the general assembly sat down at Edinburgh, anno 1643, they, upon a motion from Sir Archibald Johnston their clerk, emitted a declaration for joining with the English parliament for a variety of reasons, of which these were the sum and substance. "(1.) They apprehend the war is for religion. (2.) The protestant faith is in danger. (3.) Gratitude for the assistance in the time of the former reformation required a suitable return. (4.) Because the churches of Scotland and England being embarked in one bottom, if the one be ruined, the other cannot subsist. (5.) The prospect of an uniformity between the two kingdoms in discipline and worship, will strengthen the protestant interest at home and abroad. (6.) The present parliament had been friendly to the Scots, and might be so again. (7.) Though the king had so lately established religion amongst them, according to their desire, yet they could not confide in his royal declaration, having so often found his actions and promises contradictory the one to the other, &c." These the estates took in good part, and suggested other reasons of their own, as they saw proper.

Toward the latter end of this assembly, upon the arrival of the commissioners from the parliament and assembly at Westminster, the Scots assembly, by an act of session 14, commissioned Messrs. Henderson, Douglas, Rutherford, Bailey and Gillespie ministers, John earl of Cassils, John lord Maitland, and Sir Archibald Johnston of Warriston, ruling elders, or any three of them, whereof two should be ministers, "to repair to the kingdom of England, and there to deliver the declaration sent to the parliament of England, and the letter sent to the assembly of divines, now sitting in that kingdom, and to propound, consult, treat and conclude with that assembly, or any commissioner deputed, or any committee or commissioner deputed by the house of parliament, in all matters which may further the union of this island, in one form of church-government, one confession of faith, one catechism, one directory for the worship of God, according to the instructions they have received from the assembly, or shall receive from time to time hereafter, from the commissioners of the assembly deputed for that effect." -- This commission was again renewed by several acts of the subsequent assemblies, till the year 1648. -- And it appears, that lord Warriston did not only use all diligence as a member of the Westminster assembly, for bringing about the uniformity of religion in worship, discipline and government, but also, for some time, he sat as a member of the English parliament, for concerting such methods as might bring about a firm and lasting peace betwixt the two kingdoms afterward; which is, and was reckoned a most noble piece of service both to church and state in those days; yet we shall find it accounted high treason in this worthy man afterward.

Lord Warriston had, for his upright and faithful dealing, in the many important matters committed to his charge, received many marks of favour and dignity, both from church and state; and to crown all the rest, the Scots parliament in 1646, made an act, appointing his commission to be lord advocate, with the conduct of the committee of London and Newcastle, and the general officers of the army: all which evidence, what a noble hand he had in carrying on that blessed work of reformation.

He had now been clerk to the general assembly since the year 1638, and when that unhappy difference fell out anno 1650, when the act of classes was repeated, whereby malignants were again taken into places of power and trust; which occasioned the rise of those called protestors and resolutioners anno 1650, lord Warriston was one of those who had a principal hand in managing affairs among those faithful anti-resolutioners; for he wrote a most solid letter to that meeting at St. Andrews, July 18, 1651, concerning which, the protestors, in their reasons, proving the said meeting to be no lawful, full or free general assembly, say, "Sir Archibald Johnston, clerk to the assembly a man undeniably faithful, singularly acquainted with the acts and proceedings of this kirk, and with the matters presently in controversy, and who hath been useful above many in all the tracts of the work of reformation, from the beginning, in all the steps thereof, both at home and abroad; having written his mind to the meeting (not being able to come himself) about the things that are to be agitated in the assembly, and held out much clear light from the scriptures, and from the acts of former assemblies, in these particulars. Albeit the letter was delivered publicly to the moderator, in the face of the assembly, and urged to be read by him who presented it, that then the moderator did break it up, and caused it to be read; and that many members did thereafter, upon several occasions, and at several diets, press the reading of it, but it could never be obtained, &c.[126]"

And further, those papers bearing the name of representations, propositions, protestations, &c. were by the said lord Warriston, Messrs. Cant, Rutherford, Livingston, &c. presented to the reverend ministers and elders met at Edinburgh, July 24, 1652, when the marquis of Argyle at London procured an equal hearing to the protestors; and Mr. Simpson, one of these three ministers deposed by the assembly 1651, being sent up by the protestors for that purpose; in the beginning of 1657, Messrs. James Guthrie and Patrick Gillespie, the other three who had been deposed by that assembly, together with lord Warriston, were sent up to assist Mr. Simpson[127].

Lord Warriston had now, for the space of five years or more, wrestled and acted with all his power, for the king's interest, and, being a man of great resolution, he both spoke and wrote as openly against Scotsmen submitting to take offices under the usurper; but being sent up to London in the foresaid year 1657, with some of the Scots nobility, upon some important affairs, and Cromwel being fully sensible how much it would be for his interest to gain such a man as Warriston was, over to his side, he prevailed upon him to re-enter to the office of clerk-register; which was much lamented by this worthy man afterwards, as well as his sitting and presiding in some meeting at London after Oliver's death.

A late historian has observed, That, at that meeting at Edinburgh, which sent him up to London upon business, he reasoned against it, and to the utmost of his power opposed his being sent up, acquainting them with what was his weak side, that, through the easiness of his temper, he might not be able to resist his importunity, craving that he might not be sent among snares; and yet after all he was peremptorily named[128].

To account some way for his conduct in this: -- -- His family was numerous; and very considerable sums were owing him, which he had advanced for the public service, and a good many bygone years salaries; he was, through importunity, thus prevailed upon to side with the usurper, there being no other door open then for his relief. And yet after this his compliance, it was observed, he was generally more sad and melancholy than what he had formerly been, and it is said that his outward affairs did not prosper so well afterward.

The king being restored again to his dominions anno 1660, and the noble marquis of Argyle imprisoned July 14, orders came down to seize Sir James Stuart provost of Edinburgh, Sir Archibald Johnston of Warriston, and Sir John Chiesly of Carswel. The first and last were tried, but lord Warriston escaped for a time, and therefore was summoned, by sound of trumpet, to surrender himself, and a proclamation issued out for seizing him, promising an hundred pounds Scots to any who should do it, and discharging all from concealing or harbouring him under pain of treason. A most arbitrary step indeed! For here is not only a reward offered for apprehending this worthy gentleman, but declaring it treason for any to harbour him, and that without any cause assigned.

Upon the 10th of October following, he was, by order of the council, declared fugitive; and next year Feb.1st, the indictment against lord Warriston, William Dundas, and John Hume, was read in the house, none of them being present. Warriston was forfeited, and his forfeiture publicly proclaimed, by the heralds, at the cross of Edinburgh. The principal articles of his indictment were, his pleading against Newton Gordon, when he had the king's express orders to plead for him; His assisting to the act of the west kirk, &c.; His drawing out, contriving or consenting to the paper called the western remonstrance, and the book called the causes of the Lord's wrath; his sitting in parliament as a peer in England, contrary to his oath, &c.; His accepting the office of clerk-register from the usurper; -- -- and being president of the committee of safety, when Richard was laid aside, &c. But neither of all these were the proper causes of this good man's sufferings, but a personal prejudice or pique was at the bottom of all these bitter proceedings; for the godly freedom he took in reproving vice, was what could never be forgotten nor forgiven. The last-cited historian hints, that the earl of Bristol was interceeding for him, and says, "I have an account of this holy freedom in lord Warriston, used from a reverend minister, who was his chaplain at that time, and took freedom to advise my lord not to adventure on it; yet this excellent person, having the glory of God and the honour of religion more in his eyes than his own safety, went on in his designed reproof, and would not for a compliment, quit the peace he expected in his own conscience, be the event what it would, by disburthening himself; he got a great many fair words, and all was pretended to be taken well from my lord register; but, as he was told by his well-wishers, it was never forgot[129]." For, in compliance with Cromwel, he was not alone in the matter; the greater part of the nation being involved therein as well as he: And several of those who had been named trustees to the usurper, were all discharged from court, except Warriston, who was before come to Scotland, and ordered to appear before the parliament at the sitting down thereof.

This good man, after the sentence of forfeiture and death passed against him by the first parliament, being obliged to go abroad, to escape the fury of his enemies, even there did their crafty malice reach him; for while at Hamburg, being visited with sore sickness, it is certain that Dr. Bates, one of king Charles's physicians, intending to kill him (contrary to his faith and office), prescribed poison to him instead of physic, and then caused draw from him sixty ounces of blood, whereby (though the Lord wonderfully preserved his life) he was brought near the gates of death, and so far lost his memory, that he could not remember what he had said or done a quarter of an hour before, and continued so until the day of his martyrdom.

And yet all this did not satisfy his cruel and blood-thirsty enemies, while he was yet in life they sought him carefully; and at last, he having gone unadvisedly to France, one Alexander Murray, being dispatched in quest of him, apprehended him at Roan, while he was engaged in secret prayer, a duty wherein he much delighted. In Jan.1663, he was brought over prisoner, and committed to the tower of London, where he continued till the beginning of June, when he was sent down to Edinburgh to be executed.

His carriage during his passage was truly christian. He landed at Leith on the 8th, and was committed to the tolbooth of Edinburgh; and from thence he was brought before the parliament on the 8th of July. His nephew, Bp. Burnet, says, He was so disordered both in body and mind, that it was a reproach to any government to proceed against him[130].

When at the bar of the house, he discovered such weakness of memory and judgment, that almost every person lamented him, except Sharp and the other bishops, who scandalously and basely triumphed over, and publicly derided him; although it is well known, says a very noted author, that lord Warriston was once in case, not only to "have been a member, but a president of any judicatory in Europe, and to have spoke for the cause and interest of Christ before kings, to the stopping of the mouths of gainsayers[131]."

Here it seemed, that many of the members of parliament inclined to spare his life; but when the question was put, Whether the time of his execution should be just now fixed, or delayed, Lauderdale interposed, upon calling the rolls, and delivered a most dreadful speech for his present execution. And sentence was pronounced, That he be hanged at the cross of Edinburgh, on the 22d of July, and his head placed on the Nether-bow, beside that of Mr Guthrie. He received his sentence with such meekness as filled all with admiration; for then he desired, That the best blessings might be on church and state, and on his majesty (whatever might befal himself), and that God would give him true and faithful counsellors[132].

During the whole time of his imprisonment, he was in a most spiritual and tender frame, to the conviction of his very enemies; and the nearer that his death approached, the composure of his mind became the more conspicuous. He rested agreeably the night before his execution, and in the morning was full of consolation, sweetly expressing his assurance of being clothed with a long white robe, and of getting a new song of the Lamb's praise in his mouth. Before noon he dined with cheerfulness, "hoping to sup in heaven, and to drink the next cup fresh and new in his Father's kingdom."

After he had spent some time in secret prayer, about two o'clock he was taken from prison, attended by several of his friends in mourning, though he himself was full of holy cheerfulness and courage, and in a perfect serenity of mind. When come to the scaffold, he said frequently to the people, "Your prayers, your prayers." When he was on the scaffold he said, "I intreat you, quiet yourselves a little, till this dying man deliver his last speech among you;" and desired they would not be offended at his making use of the paper to help his memory, so much impaired by long sickness and the malice of physicians. Then he read his speech first on the one side of the scaffold, and then on the other. In which speech, after a a short preamble, shewing that that which he intended to have spoken at his death, was not now in his power, being taken from him, yet hoped the Lord would preserve it to be his testimony; being now for some time in a most melancholy concumitance, through long and sore sickness, drawing of blood, &c. He, in the first place, confesseth his sins, pleads for forgiveness, bewails his compliance with the usurper, although, said he, he was not alone in that offence, but had the body of the nation going before him, and the example of all ranks to insnare him, &c. Then declares his adherence to the covenanted work of reformation, earnestly desiring the prayers of all the Lord's praying people, &c. and vindicates himself from having any accession to the late king's death, and to the making of the change of government; taking the great God of heaven to witness between him and his accusers. And at last concluded with these words, "I do here now submit, and commit my soul and body, wife and children, and children's children, from generation to generation for ever, with all others his friends and followers, all his doing and suffering witnesses, sympathizing ones in present and subsequent generations, unto the Lord's choice mercies, graces, favours, services, employment, enjoyments and inheritments on earth and in heaven, in time and all eternity; all which suits, with all others which he hath at any time, by his Spirit, moved and assisted me to put up, according to his will, I leave before and upon the Father's merciful bowels, the Son's mediating merits, and the Holy Spirit's compassionate groans, both now and for ever more Amen[133]."

After the reading of his speech, he prayed with great fervency and liberty, and, being in a rapture, he began thus, "Abba, Father! Accept this thy poor sinful servant, coming unto thee, through the merits of Jesus Christ, &c." Then taking leave of his friends, he prayed again with great fervency, being now near the end of that sweet work, he had so much, through the course of his time, been employed in. No ministers were allowed to be with him, but it was, by those present, observed that God sufficiently made up that want. He was helped up the ladder by some of his friends in deep mourning; and, as he ascended, he said, "Your prayers, your prayers. -- Your prayers I desire in the name of the Lord." -- Such was the esteem he had for that duty.

When got to the top of the ladder, he cried out with a loud voice, "I beseech you all who are the people of God, not to scare at suffering for the interest of Christ, or stumble at any thing of this kind, falling out in these days; but be encouraged to suffer for him, for I assure you in the name of the Lord, he will bear your charges." While the rope was putting about his neck, he repeated these words again, adding, The Lord hath graciously comforted me. When the executioner desired his forgiveness he said, The Lord forgive thee, poor man, -- and withal gave him some money, bidding him do his office if he was ready; and crying out, O pray, pray! Praise, praise, praise, -- he was turned over, and died almost without any struggle, with his hands lifted up unto heaven, whither his soul ascended, to enjoy the beatific presence of his Lord and Saviour Jesus Christ.

He was soon cut down, and his head struck off, and set up beside that of his dear friend Mr. Guthrie; and his body carried to Gray-friars church-yard. But his head soon after, by the interest and intercession of lieutenant-general Drummond (who was married to one of his daughters), was taken down and interred with his body.

Thus stood and thus fell the eminently pious and truly learned lord Warriston, whose talents as a speaker in the senate, as well as on the bench, are too well known to be here insisted upon; and for prayer, he was one among a thousand, and oftimes met with very remarkable returns; and though he was for some time borne down with weakness and distress, yet he never came in the least, to doubt of his eternal happiness, and used to say, "I dare never question my salvation, I have so often seen God's face in the house of prayer." And, as the last cited historian observes, "Although his memory and talents were for some time impaired, yet like the sun at his setting, after he had been a while under a cloud, shone most brightly and surprizingly, and so in some measure the more sweetly; for that morning he was under a wonderful effusion of the Spirit, as great perhaps as many have had since the primitive times."

He wrote a large diary, which yet remains in the hands of his relations, and in which is a valuable treasure both of christian experience, and matters of fact little known at present, which might be of great use and light to the history of that period, and wherein he records his sure hopes (after much wrestling in which he was mightily helped) that the church of Scotland would he manifestedly visited and freed from the evils she fell under after the restoration. And his numerous family, whom he so often left upon the Lord's providence, were, for the most part, as well provided for as could have been expected, though he had continued with them in his own outward prosperity. He that overcometh, shall be clothed in white raiment, and I will not blot out his name out of the book of life: but I will confess his name before my Father and his angels.