CHAPTER 1 -

• fta1 Burnet’s History of the Reformation, vol. 1. p. 125.
• fta2 Burnet’s Hist. Ref., vol. 3 p. 144.
• fta3 Burnet’s Hist. Ref., vol. 3 p. 151.
• fta4 Burnet’s Hist. Ref., vol. 1 pp. 333-338.
• fta5 Burnet’s Hist. Ref., vol. 1 pp. 400, 401.
• fta6 Burnet’s Hist. Ref., vol. 2 pp. 116, 127.
• fta7 Ibid., vol. 2 p. 179.
• fta8 Ibid., vol. 2 p. 245, et seq .
• fta9 Burnet’s Hist. Ref., vol. 3 pp. 808, 810.
• fta10 Ibid., vol. 2 p. 326.
• fta11 Burnet’s Hist. Ref., vol. 3 p, 280.
• fta12 M’Crie’s Life of Knox, pp, 86, 87; Neale’s History of the Puritans, vol. 1 pp. 76-82.
• fta13 In the queen’s injunctions, subsequently issued, an explanation was given of the oath of supremacy; in which her majesty declared that she did not pretend to any authority for the ministering of divine service in the Church, and that all that she claimed was that which at all times belonged to the imperial crown of England; — that she had the sovereignty and rule over all manner of persons, under God, so that no foreign power had rule over them. If the oath of supremacy had implied no more than the plain meaning of these words, it would scarcely have been disputed by any; but it would have been ineffectual for the purpose for which it was intended, and it would not have sanctioned much that was done under its authority.
• fta14 The leading men of the first race of Puritans were, Bishops Jewell, Grindal, Horn, Sandys, Pilkington, Parkhurst, and Guest; also Miles Coverdale, Fox, Dr. Humphreys, Mr. Sampson, and many others of scarcely inferior reputation. Even Parker at Grat opposed the episcopal vestments, and was consecrated without them.
• fta15 Burnet’s Hist. Ref., vol. 3 p. 424.
• fta16 In proof of this, see Life of Knox, Note R.
• fta17 Burnet, vol. 3 p. 443.
• fta18 Burnet’s Hist. Ref., vol. 3 p. 464.
• fta19 Strype’s Life of Parker, p. 155.
• fta20 Strype’s Life of Parker, p. 215.
• fta21 M’Crie’s Life of Knox, p. 295.
• fta22 Strype’s Life of Parker, p, 241.
• fta23 Strype’s Life of Grindal, pp. 115, and 135, 136.
• fta24 In none of the MSS copies of the Thirty-nine Articles, either as passed by the Convocation of 1562, or as ratted by the Parliament of 1571, is the clause in the 20th article to be found, by which the Church of England claims the power “to decree rites and ceremonies.” It must have been surreptitiously introduced afterwards by some of the Prelatic party, without civil or ecclesiastical authority. — See Historical and Critical Essays on the Thirty-nine Articles , pp. 277-279.
• fta25 Strype’s Life of Parker, p. 395.
• fta26 Strype’s Life of Grindal, pp. 175, 176.
• fta27 Neal, vol. 1 p. 198; Collier, vol. 2 p. 541.
• fta28 Strype’s Life of Grindal, p. 221.
• fta29 Neal, vol. 1 pp. 245-247; Fuller, vol. 3 pp. 61-65.
• fta30 Neal, vol. 1 pp. 260-263; Fuller, vol. 3 p. 68.
• fta31 Life of Whitgift, p. 198.
• fta32 Neal, vol. 1 pp. 314, 315.
• fta33 Life of Whitgift, p. 292; Collier, vol. 2 p. 609; Neal, vol 1 pp. 321-323.
• fta34 Fuller, vol. 3 pp. 143-146.
• fta35 Fuller, vol. 3 pp. 147-150.
• fta36 Fuller, vol. 3 p. 172; Collier, vol. 2 p. 672; Neal, vol. 1 pp. 871, 392.
• fta37 Hampton Court Conference, p. 23.
• fta38 Ecclesiastical History, vol. 3 p. 482.
• fta39 Hampton Court Conference, pp. 93, 94.
• fta40 Neal, vol. 1 pp. 416, 417.
• fta41 Neal, vol. 1 pp. 461, 462.
• fta42 Fuller, vol. 3 pp. 270-273.
• fta43 Rapin, vol. 2 pp. 192, 193.
• fta44 Rapin, vol. 2 p. 212.
• fta45 Rushworth, vol. 1 p. 192; Whitelocke, p. 2.
• fta46 Rushworth, vol. 1 p. 659, et seq .
• fta47 In passing sentence on Bastwick, the bishops denied that they held their jurisdiction from the king. — Whitelocke , p. 22.
• fta48 Whitelocke, p. 24.
• fta49 Neal, vol. 1 p. 618.
• fta50 Neal, vol. 1 pp. 584, 585.
• fta51 Neal, vol. 1 p. 630.
• fta52 Whitlocke, p. 36.
• fta53 Whitelocke, p. 43.
• fta54 Whitelocke, p. 43.
• fta55 Ibid.; Rushworth, vol. 4 p. 241.
• fta56 The committee were, the Earl of Bedford, Lord Howard, Sir Philip Stapleton, Sir William Armyne, Mr. Hampden, and Mr. Fiennes.
• fta57 Baillie’e Letters, vol. 1 p. 392; Brodie’s British Empire, vol. 3 pp. 150- 155.
• fta58 The perusal of “A Declaration of the Commons,” etc., July 25, 1642, would prove to any impartial reader that there was such a plot between the queen and the Irish Papists, and that the king knew of it.
• fta59 Rushworth, vol. iv. pp. 438-451; Whitelocke, p. 49.
• fta60 Whitelocke, p. 51.
• fta61 Whitelocke, p. 50.
• fta62 Rushworth, vol. 4 p. 567.
• fta63 Clarendon, vol. 2 p. 720.
• fta64 Acts of Assembly, 1642.
• fta65 Neal, vol. 2 pp. 150, 151.
• fta66 Rushworth, vol. 5 pp. 337-339.

CHAPTER 2 -

• ftb1 Lightfoot’s Works, vol. 13 pp. 3, 4.
• ftb2 Baillie, vol 2 pp. 108, 109.
• ftb3 Lightfont, p. 5.
• ftb4 Clarendon.
• ftb5 Fuller, vol. 3 p. 448.
• ftb6 For the use of perhaps the most complete collection of these sermons extant, the author is indebted to the kindness and courtesy of the Rev. Mr. Craig of Rothsay.
• ftb7 Baillie, vol. 2 p. 80.
• ftb8 Ibid., vol. 2 p. 89. All the documents referred to, with their answers, may be seen in the Acts of Assembly 1643.
• ftb9 The Lord High Commissioner, Sir Thomas Hope, declined assenting to the Covenant in his official capacity, but personally he gave his cordial concurrence.
• ftb10 See Appendix.
• ftb11 The angry language of Dr. Lightfoot is positively ludicrous: — “A wretch that ought to be branded to all posterity, who seeks, for some devilish ends, either of his own or others, or both, to hinder so great a good of the two nations.” — Lightfoot , vol. 13 p, 12.
• ftb12 Rushworth, vol. 5 p. 475.
• ftb13 This roll was subscribed by two hundred and twenty-eight members of the House of Commons, whose names may be seen in Rushworth, vol. 5 pp. 480, 481. On that roll appears the name of Oliver Cromwell.
• ftb14 Rushworth, vol. 5 p. 482.
• ftb15 Neal, vol. 2 pp. 284,235.
• ftb16 Brook’s Lives of the Puritans, vol. 3 p. 312.
• ftb17 Brook, vol. 2 p. 454; Edward’s Antapologia, pp. 115-117; Baillie’s Dissuasive, pp. 75-77.
• ftb18 Baillie, vol. 2 p. 110.
• ftb19 Neal, vol. 2 pp. 275, 360.
• ftb20 Palmer’s Nonconformist’s Memorial, vol. 1 p. 96.
• ftb21 “John Lillburn related it unto me, and that in the presence of others, that returning from the wars to London, he met forty new sects, many of them, dangerous ones, and some so pernicious, that howsoever, as he said, he was in his judgment for toleration of all religions, yet he professed he could scarce keep his hands off them, so blasphemous they were in their opinions.” — Bastwick ’s Second Part of Independency , postscript, p. 37. Lillburn was himself a Leveler.
• ftb22 We shall have occasion, in a subsequent part of this work, to prove that the true idea of toleration, in its right moral and religious sense, was first taught and first exemplified by the Presbyterian Church of Scotland, next by the Puritans, and then adopted, but corrupted, by the Sectarians and Independents.

CHAPTER 3 -

• ftc1 Baillie, vol. 2 p. 104.
• ftc2 Lightfoot, p. 20.
• ftc3 Lightfoot, p. 23.
• ftc4 Lightfoot, pp. 53, 58; Baillie, vol. 2 p. 110.
• ftc5 Lightfoot, p. 76.
• ftc6 Baillie, vol. 2 p. 111.
• ftc7 Lightfoot, p. 78.
• ftc8 Lightfoot, p. 24.
• ftc9 Lightfoot, p. 57; Baillie, vol. 2 p. 111.
• ftc10 Lightfoot, p. 62.
• ftc11 First Century, etc.
• ftc12 Lightfoot, pp. 100-102; Baillie, vol. 2 p. 129.
• ftc13 Lightfoot p. 113.
• ftc14 Lightfoot, p. 115.
• ftc15 Lightfoot, p. 117.
• ftc16 Ibid., p. 130.
• ftc17 Lightfoot, pp. 230-233. The conduct and language of the Scottish divines in this debate prove clearly that they held the principle of election by the people to be the right one; and that the utmost modification of it to which they could consent was, that no man be intruded. They were, in short, what would now be termed “decided Non-Intrusionists,” at the least; and their consent to a modified proposition was caused by their dread of the sectarian confusion then prevalent in England.
• ftc18 Baillie, vol. ii. pp. 198 and 221.
• ftc19 Rushworth, vol. v. p. 780.
• ftc20 Rushworth, vol. 5 p. 781. The names of the Assembly divines were, Drs. Burgess and Gouge, Messrs Walker, Conant, Cawdry, Calamy, Chambers, Ley, Gower, and Roborough. The city ministers were, Messrs Downham, Dod, Clendon, Bourne, Roberts, Offspring, Crauford, Clarke, Billets, Cooke, Lee, Horton, and Jackson. A similar committee was also appointed for the county of Lancaster. — Neal , vol. 2 p. 273.
• ftc21 Baillie, vol. 2 p. 242.
• ftc22 Lightfoot, p. 115.
• ftc23 Lightfoot, p. 119.
• ftc24 Ibid., p. 126.
• ftc25 Baillie, vol. 2 p. 137.
• ftc26 Baillie, vol. 2 p. 130.
• ftc27 Apologetical Narration, pp. 3, 4.
• ftc28 Apol. Nar., pp. 23, 24.
• ftc29 Lightfoot, p. 132.
• ftc30 Lightfoot, pp. 132-134.
• ftc31 Lightfoot, p. 144.
• ftc32 Ibid., p. 147.
• ftc33 Lightfoot, p. 151.
• ftc34 Lightfoot, pp. 165-168.
• ftc35 Wodrow’s Analecta; M’Crie’s Sketches, p. 300; Appendix.
• ftc36 Lightfoot, pp. 168-170; Baillie, vol. 2 pp. 146, 147; Appendix, Nye.
• ftc37 Lightfoot, pp. 214, 215.
• ftc38 Lightfoot p. 229.
• ftc39 Baillie, vol. 2 p. 148.
• ftc40 Appendix, Nye.
• ftc41 Lightfoot, p. 250.
• ftc42 Lightfoot, pp. 255, 256; Baillie, vol. 2 p. 177.
• ftc43 Lightfoot, p. 262.
• ftc44 Ibid., p. 267.
• ftc45 Lightfoot, p. 268.
• ftc46 Baillie, vol. 2 pp. 226, 230.
• ftc47 Papers for Accommodation, page 1.
• ftc48 Reasons of the Dissenting Brethren, p. 124.
• ftc49 Reasons and Answers, p. 138.
• ftc50 Ibid., p. 147.
• ftc51 Reasons of Dissent, pp. 190, 191.
• ftc52 Answer to a Copy of a Remonstrance, page 16.
• ftc53 Answer to a Copy of a Remonstrance, p. 19; Baillie, vol. 3 pp. 266, 267.
• ftc54 Baillie, vol. 3 p. 344.
• ftc55 Answer to a Copy of a Remonstrance, p. 24.
• ftc56 Baillie, vol. 2 p. 183.
• ftc57 Palmer’s Nonconformist’s Hemorial, vol. 1 p. 96; Appendix, Nye.
• ftc58 This I hold myself quite at liberty to state, from a careful perusal of the writings of these pious men; and especially from Goodwin’s work “On the Constitution, Right, Order, and Government, of the Churches of Christ,” in the fourth volume of his works; which seems to be the result of his attempt to frame a model of the Independent system of Church government, and which, with all its defects, shows much of a Christian Spirit and temper.

CHAPTER 4 -

• ftd1 Baillie, vol. 2 p. 266.
• ftd2 Lightfoot, p. 106.
• ftd3 Lightfoot, pp. 153, 154.
• ftd4 Lightfoot, pp. 165, 166.
• ftd5 See before, pp. 201, 202; also Appendix.
• ftd6 Whitelocke, p. 95.
• ftd7 Baillie, vol. 2 p. 198.
• ftd8 Lightfoot, p. 323.
• ftd9 Whitelocke, p. 106.
• ftd10 The account of this matter given by Neal is worse than inaccurate. He says, “When the question was put, it was carried in the negative;” whereas it was only “laid aside,” not negatived. Neal thought it a victory over the Presbyterians, — hence his misrepresentation.
• ftd11 Whitelocke, pp. 130, 131.
• ftd12 Whitelocke, p. 134.
• ftd13 Baillie, vol. 2 p. 267.
• ftd14 Whitelocke, p. 158.
• ftd15 Ibid., p. 160.
• ftd16 Whitelocke, p. 163; Rushworth, vol. 6 p. 203.
• ftd17 Whitelocke, pp. 163, 164; Rushworth, vol. 6 pp. 203-205.
• ftd18 Baillie, vol. 3 p. 307.
• ftd19 Whitelocke, p. 159.
• ftd20 Baillie, vol. 2 p. 325.
• ftd21 Whitelocke, p. 162.
• ftd22 Rushworth, vol. 6 pp. 210-212. See Appendix.
• ftd23 Whitelocke, p. 187.
• ftd24 Whitelocke, p. 194.
• ftd25 Rushworth, vol. 6 pp. 224-228. See Appendix.
• ftd26 Rushworth, vol. 6 pp. 254, 255.
• ftd27 Baillie informs us that David Buchanan was the person by whom they were published. Vol. 2 p. 367.
• ftd28 This was evidently for the purpose of intimidation.
• ftd29 Rushworth, vol. 6 pp. 260, 261.
• ftd30 Baillie, vol. 2 p. 360.
• ftd31 Neal, vol. 2 p. 395.
• ftd32 Baillie, vol. 2 p. 378. — This is a sufficient refutation of Neal’s assertion, that the Assembly durst not present their answers to Parliament for fear of a premunire .
• ftd33 Baillie, vol. 2 p. 411.
• ftd34 A reprint of this work would be a very valuable contribution to the Presbyterian cause in the present day.
• ftd35 Whitelocke, p. 213.
• ftd36 Baillie, vol. 2 p. 377; Neal, vol. 2 p. 396. In this instance also the Account of Neal is unfair and inaccurate, to use no harsher terms.
• ftd37 Whitelocke, p. 210.
• ftd38 Ibid.
• ftd39 Whitelocke, p. 211.
• ftd40 Baillie, vol. 2 p. 391.
• ftd41 Whitelocke, pp. 225, 226.
• ftd42 Rushworth, vol. 6 p. 476.
• ftd43 Whitelocke, pp. 275, 276.
• ftd44 Baillie, vol. 2 p. 325.
• ftd45 Whitelocke, p. 233.
• ftd46 Rushworth, vol. 6 p. 473.
• ftd47 Rushworth, vol. 12 p. 1035.
• ftd48 Neal, vol. 2 p. 429.
• ftd49 Lightfoot, vol. 1 p. 165.
• ftd50 Coleman’s Sermon, pp. 24-28.
• ftd51 Baillie, vol. 2 p. 246.

CHAPTER 5 -

• fte1 Baillie, vol. 2 p. 379.
• fte2 Baillie, vol, 2 p. 148.
• fte3 Reid’s Lives of the Westminster Divines, vol. 2 p. 214.
• fte4 Baillie, vol. 3 p. 2.
• fte5 Neal, vol. 2 p. 431.
• fte6 Neal, vol. 2 pp. 690-692.
• fte7 For a full account of this Conference, see History of Nonconformity, Life of Baxter, etc.
• fte8 One of these the author was fortunate enough to assist in rescuing from the hands of Socinians, a few years ago, on the strength of that very condition.
• fte9 “Some, perhaps, by a toleration understand an universal , uncontrolled license of living as you please in things concerning religion: that every one may be let alone , and not so much as discountenanced in doing, speaking, acting, how, what, where, or when he pleaseth, in all such things as concerneth the worship of God, articles of belief, or generally any thing commanded in religion; and in the meantime, the parties at variance, and litigant about differences, freely to revile, reject, and despise one another, according as their provoked genius shall dispose their minds thereunto. Now, truly, though every one of this mind pretends to cry for mercy to be extended unto poor afflicted Truth , yet I cannot but be persuaded that such a toleration would prove exceeding pernicious to all sorts of men.” — Essay by Dr . Owen , appended to a Sermon preached before the House of Commons, April 29, 1646; p. 66.
• fte10 Answer to Stillingfleet’s Unreasonableness of Separation. Works, vol. 15 p. 433, Johnstone & Hunter’s edition.
• fte11 “The Principles of Faith presented by Mr. Thomas Goodwin, Mr. Nye, Mr. Simpson, and other Ministers, to the Committee of Parliament for Religion, etc. “ 1. That the Holy Scripture is that rule of knowing God, and living unto him, which whoso does not believe cannot be saved. “ 2. That there is a God, who is the Creator, Governor, and Judge of the world, — which is to be received by faith; and every other way of the knowledge of him is insufficient. “ 3. That this God, who is the Creator, is eternally distinct from all creatures, in his being and blessedness. “ 4. That this God is one, in three persons or subsistences. “ 5. That Jesus Christ is the only Mediator between God and man, without the knowledge of whom there is no salvation. “ 6. That this Jesus Christ is the true God. “ 7. That this Jesus Christ is also true man. “ 8. That this Jesus Christ is God and man in one person. “9. That this Jesus Christ is our Redeemer, who, by paying a ransom, and bearing our sins, has made satisfaction for them. “ 10. That this same Jesus Christ is he that was crucified at Jerusalem, and rose again, and ascended into heaven. “ 11. That this same Jesus Christ, being the only God and man in one person, remains for ever a distinct person from all saints and angels, notwithstanding their union and communion with him. “ 12. That all men by nature are dead in trespasses and sins; and no man can be saved unless he be born again, repent, and believe. “ 13. That we are justified and saved by grace, and faith in Jesus Christ, and not by works. “ 14. That to continue in any known sin, upon what pretense or principle soever, is damnable. “ 15. That God is to be worshipped according to his own will; and whosoever shall forsake and despise all the duties of his worship cannot be saved. “ 16. That the dead shall rise; and that there is a day of judgment, wherein all shall appear, some to go into everlasting life, and some into everlasting condemnation.” — Neal , vol. ii. pp. 621, 622.
• fte12 Lightfoot, p. 86.
• fte13 Baillie, vol. 2 p. 192.