"Is God, alone, Lord of the conscience, and hath left it free from the doctrines and commandments of men, which are in any thing contrary to his word, or beside it, in matters of faith or worship?"

Yes.

James 4.12. Acts 4.19. Acts 5.29. Matt. 23.8-10. 2 Cor. 1.24. Matt. 15.6.

Well then, do not the Papists err, who contradict this, both in doctrine (because they teach that the pope of Rome, and bishops in their own dioceses, may, by their own authority, præter Scripturam, besides the word make laws which oblige and bind the conscience, under pain of everlasting death); and in practice, (because they have obtruded, and do obtrude many ecclesiastical rites and ceremonies, as necessary in worship, without any foundation in scripture?)

Yes.

By what reasons are they confuted?

1st, Because there is one lawgiver, who is able to save and to destroy, James 4.12. Therefore no pope, no prelate, nor any mere man, can be a lawgiver.

2d, Because Christ rejects the commandments of men for the worship of God, Matt. 15.9.

3d, Because the apostles refused to obey the orders of their council, since they were contrary to the commands of God, Acts. 4.19. and 5.29.

4th, Because the Lord threatens to do a marvelous work among his people, because they drew near to him with their mouth, (as the most part of the ceremonial service is but a drawing near to God with the mouth,) but had their hearts removed far from him, Isa. 29.13,14.

5th, Because Christ expressly forbids such subjection and obedience to the commands of men, Matt. 23.9,10. 1 Cor. 7.23.

6th, Because the apostles themselves forbid all will-worship, such as the Papists ceremonies are, Col. 2.18,21-23.

7th, Because the apostle Paul withstood these false brethren, unawares brought in, who cam in privily, to spy out his liberty which he had in Christ Jesus, that they might bring him into bondage, to whom he gave place by subjection, no not for an hour, that the truth of the gospel might continue; where he lays so much weight upon Christian liberty, that if that were taken away, the truth of the gospel would perish likewise, Gal. 2.4,5.

8th, Because the apostle commands believers to stand fast in their liberty, wherewith Christ hath made them free, and not to be entangled again with the yoke of bondage, Gal. 5.1.

9th, Because ceremonies are superstitious, being a vice opposite to religion in the excess, commanding more in the worship of God, than he requires.

Quest. II. "Is not the requiring of an implicit faith, and an absolute and blind obedience to the church, or any man, a destroying of liberty of conscience, and reason also?"

Yes; Rom. 10.17. and 14.23. Isa. 8.20. Acts 17.11. John 4.22. Hos. 5.11. Rev. 13.12,16,17. Jer. 8.9.

Well then, do not the Papists err, who require an implicit faith to all the decrees and ordinances of their church and pope; and a blind obedience to their commands, without a previous judgment of discretion?

Yes.

By what reasons are they confuted?

1st, Because no man performing any duty out of blind obedience, can be persuaded in his mind of the will of God therein; and so he that doubteth is damned, because it is not of faith, Rom. 14.23.

2d, Because all things must be examined and proved by the rule of the word, Isa. 8.20. 1 John. 4.1,2.

3d, Because the apostle says, Prove all things, and hold fast that which is good, 1 Thes. 5.21.

4th, Because blind obedience makes us the servants of men, which is contrary to 1 Cor. 7.23. And against the command of Christ, forbidding us to call any man Father on earth, Matt. 23.9.

5th, Because absolute obedience is only due to God, whose commands are all most just, himself being the alone lawgiver, James 4.12.

6th, Because every man ought to be ready to render a reason of the hope which is in him, 1 Pet. 3.15. This no man can do, who receives the commands of superiors with an implicit faith.

Quest. III. "Do they who upon pretence of Christian liberty, practice any sin, or cherish any lust, destroy thereby the end of Christian liberty?"

Yes; Gal. 5.13. 1 Pet. 2.16. 2 Pet. 2.19. John 8.34. Luke 1.74,75.

Well then, do not the Libertines err, who maintain, That true Christian liberty, which we ought to follow and use, is to take away all difference between good and evil; To esteem nothing of sin, nor to be touched with any conscience or sense of it; that every man ought to follow the swing of his own lusts?

Yes.

Do not likewise the Antinomians err, who maintain, almost, the same very tenet and opinion?

Yes.

By what reasons are they confuted?

1st, Because we being called to liberty, ought not to use our liberty for an occasion of the flesh, Gal. 5.13. And that with well doing, we ought to put to silence the ignorance of foolish men, 1 Pet. 2.15.

2d, Because they that follow the liberty of sinning, and promise liberty to others, are truly the servants of corruption: For of whom a man is overcome, of the same is he brought in bondage, 2 Pet. 2.19.

3d, Because the end of that liberty which is purchased by Christ, is, that being delivered out of the hands of our enemies, we might serve him without fear, in holiness and righteousness, all the days of our life, Luke 1.74,75.

4th, Because whosoever committeth sin is the servant of sin, John 8.34.

5th, Because the moral law obligeth believers to perform obedience, out of gratitude and thankfulness; for Christ came not to destroy the law, but to fulfill it, Matt. 5.17.

6th, Because whosoever shall break one of these least commandments, and shall teach men so, he shall be called the least in the kingdom of heaven, Matt. 5.19.

Quest. IV. "May such men be lawfully called to an account, and proceeded against by the censures of the church, and by the power of the civil magistrate, who publish such opinions, or maintain such practices, as are contrary to the light of nature, or to the known principles of Christianity, whether concerning faith, worship, or conversation, or to the power of godliness, or such erroneous opinions and practices, as either in their own nature, or in the manner of publishing or maintaining them, are destructive to the external peace and order, which Christ hath established in his church?"

Yes; 1 Cor. 5.1,5,11,13. 2 John 10,11. 1 Tim. 6.3,4. Titus 1.10,11,13. Titus 3.10. 1 Tim. 1.19.20. Matt. 18.15-17. Rev. 2.2,14,15,20. Rev. 3.9.

Well then, do not the Anabaptists err, who maintain, There should be no ecclesiastical censures?

Yes.

Do not others also err, who maintain, That church censure should not be inflicted upon heretics?

Yes.

Do not lastly, the Lutherans, Anabaptists, Arminians, Quakers, and all sorts of heretics and sectaries err, who maintain, under pretext of Christian liberty, That the civil magistrate is not in duty to punish any man with the sword, for errors in doctrine, but that they ought to be tolerated and suffered, provided such persons as own them, do not trouble or molest the common-wealth?

Yes.

By what reasons are they confuted?

1st, Because the keys of the kingdom of heaven, are for this end delivered to the ministers of the church, that with censures they may pursue scandalous and offending persons, who will not obey admonition, Matt. 18.15,17,18.  But such also are heretics, Gal. 5.20. Titus 1.10,12.

2d, Because an heretic, after the first and second admonition, is to be rejected, avoided, or shunned. That is, let him not remain in the external communion of the church, Titus 3.10.

3d, Because Paul did excommunicate Hymeneus and Alexander, who had made shipwreck of the faith, 1 Tim. 1.19,20.

4th, Because if any man obey not our word by this epistle, note that man, and have no company with him, that he may be ashamed, 2 Thes. 3.14. 1 Tim. 6.4,5. Titus 1.11.

5th, Because Christ approves and commends the pastors of the church of Ephesus, because they could not suffer them that are evil; but had tried them which say they are apostles, and were not, and had found them liars, Rev. 2.2. And Christ, in that same chapter, accuses the pastors of the church of Pergamus and Thyatira, and threateneth them, because they had suffered heretics to be in the church.

The Lutherans, Anabaptists, Arminians, and other sectaries are confuted.

1st, Because it is evident from many examples of godly magistrates, who did extirpate idolatry, and inflict punishment upon idolaters; as did Jacob the patriarch, who purged his family of strange gods, Gen. 35.2-4. Moses likewise took punishment with the sword, upon those who did worship the golden calf, Exod. 32.26-28. We have

2d, The example of Hezekiah, 2 Kings 18.4. Of Josiah, 2 Kings 23. Of Asa, who decreed, that whosoever would not seek the Lord God of Israel (according to the law of God, Deut 13.9.) should be put to death, whether small or great, whether man or woman, 2 Chron. 15.13. Of Jehosaphat, 2 Chron. 17.6. Of Nehemiah, chap. 13.15,17,25.

3d, Were not good kings reproved, and was it not imputed to them as a fault, that they did not take away the high places? 2 Kings 12.3, 14.4, 15.4. 2 Chron. 15.17. Far more is it a fault to suffer heretics.

4th, It is evident from the office of the magistrate, who is the minister of God against them that do evil, and bears not the sword in vain, Rom. 13.4.

5th, Because it is expressly commanded in Scripture, that punishment be inflicted upon idolaters, even by the nearest relations. If then, the father may kill the Son, may kill the daughter; the husband the wife of his bosom; and if one brother may stone another brother with stones that he die, for being idolaters; much more may the civil magistrate do this, Deut. 13.6-13. Deut. 17.2-7. Lev. 24.16.

6th, Because it is foretold, that under the New Testament, kings shall be nursing fathers to the church, and queens nursing mothers; and that heretics that were about to be hurtful to the church, shall be removed and taken away, Isa. 49.23. Zech. 13.2,3. And it shall come to pass in that day, saith the Lord of hosts, that I will cut off the names of the idols out of the land, (that is all idolatry whatsoever, so that the same shall not be so much as named any more among you) and they shall no more be remembered. And I will also cause the prophets, (the false prophets) and the unclean spirit to pass out of the land; (that is, the false teachers who teach impure doctrines, thro' the inspiration of the unclean spirit the devil.) Compare this with 1 John 4.1-3. For confirmation, consider what is foretold by John, Rev. 17.12,16,17. That the kings of the earth shall eat the flesh of the whore, and burn her with fire. All which are foretold, as blessings to be conferred upon the church.

7th, It is evident from the epithets whereby the pernicious and destructive nature of heretics is set forth in scripture. They are called wolves, not sparing the flock, thieves, robbers, troublers of the church, and seducers or beguilers of poor souls. They are like unto a gangrene, or canker in the body. They are as leaven, or sour dough, which leaveneth the whole lump, Acts 20.29. John 10.8. Acts 15.24. Gal. 5.12. 2 Tim. 2.17. Gal. 5.9.

8th, Because Ezra did esteem it a great favour and blessing of God conferred upon the church; for which he thanked God, that had inclined the heart of Artaxerxes to publish a decree for the punishment of those that did not observe the law, whether it be, saith the text, unto death, or to banishment, or to confiscation of goods, or to imprisonment, chap. 7.23,25,28.

9th, Because we ought to pray for kings, and all in authority, that under them we may lead a quiet and peaceable life in all godliness, and in honesty, which end cannot be attained unless the civil magistrate bridle and tie up heretics, 1 Tim. 2.2. these words, in all godliness, concern religion, or the first table of the moral law, as the following word, honesty, or civility, hath a respect to the commands of the second table, and the duties which we owe to our neighbour and to one another. For true magistrates are keepers and defenders of both tables of the ten commandments.

10th, Because the toleration of heretics, as we may read of the Anabaptists in Germany, Thomas Muntzer, John of Leyden, and their followers, first by railing against the ministry, as the Quakers do, and by raging against the magistracy, brought both church and state into confusion, put the country into burning flames, wherein themselves at length were consumed to ashes.