First, For practices of this kind, there is nothing more common in scripture history.
1. I shall begin at the first war that is recorded in the world: wherein some lots fell to the godly at first, but afterwards by the virtue and valour of their brethren they were vindicated, and the victory recovered with honour. Lot, and his family living in Sodom, was taken prisoner, by Chedarlaomer and his confederates, Gen. xiv. 12. but Abraham hearing of it, armed his trained his servants, and pursued them to Dan, and rescued him, ver. 14,—19. thereby justifying that rebellion of the cities of the plain, by taking part and vindicating the rebels. Hence, he that may rescue subjects from the violence of any tyrannizing domination by arms, may also rise with these subjects to oppose that violence; but here is an example of that in Abraham:—therefore,
2. After the Lord's people were possessed of Canaan, and forgetting the Lord, did enter into affinity with these interdicted nations, some of them were left to prove Israel, that the generations of the children of Israel might know to teach them war, Judg. iii. 1, 2. And when they did evil in the sight of the Lord, he sold them into the hand of Cushan Rishathaim, king of Mesopotamia, whom they served and were subject to eight years, vers. 8. but when they cried unto the Lord, their rebellion, shaking off that yoke, was successful under the conduct of Othniel, vers. 10. And after a relapse unto the like defection, they became subject to Eglon king of Moab, whom they served eighteen years, vers. 14. but attempting the same remedy by arms, under the conduct of Ehud, they recovered their liberty. And after his death, falling into that sin again, which procured the like misery, they became subject to Jabin king of Canaan, who twenty years mightily oppressed them, Judg. iv. 1-3. but by the Lord's commandment, under the conduct of Deborah and Barak, they rebelled and prevailed. Whence, if the Lord's people serving a sovereign domineering power, may shake off the yoke of their subjection: then it is duty to defend themselves and resist them, for there is no other way of shaking it off; but these examples prove the former: therefore,—Obj. If any cavil that these were not their own kings, to whom they owed allegiance, but only invading conquerors, whom they might resist. I answer, (1.) Yet they were the sovereign powers for the time; and therefore, if royalists and loyalists grounds hold good, they ought upon no pretence whatsoever to have been resisted: and though possibly they might not be by compact their own kings, yet by conquest they were, as much as that would make them, and by their own consent, when they paid them king's due, viz. tribute, (2.) No more are they our kings, who either intrude themselves into an arbitrary domination over us, (without any terms of a compact upon a pretence of hereditary succession) or being our covenanted kings overturn all the conditions of their compact, and degenerate into tyrants: to such we owe no allegiance, more than Israel did to these dominators. (3.) I retort that old Colewort twice boiled, who should be judge, whether they were their own lawful kings or not? For they acted as kings, and thought themselves their absolute lords, and gave themselves out to be such; and yet we find an approved rebellion against them. Mr. Gee, in his Magistrate's Original, chap. 8. Sect. 4. Pag. 268. improves these instances to the same purpose; and adds, 'Neither (as far as my observation goes) can any immediate or extraordinary command or word for what they so did be pretended to, or pleaded from the text, for many of them, or for any, save Barak or Gideon.'
3. Yet Gideon's example, though he had an extraordinary call, cannot be pretended as unimitable on the matter; for that was ordinary, though the call and manner was extraordinary. He, with the concurrence of a very few men, did break the yoke of subjection to Midian, Judg. vi. and vii. chap. and having called his brethren out of all mount Ephraim, into a conjunction with him in the pursuit of his victory; when he demanded supply of the princes of Succoth, and of the men of Penuel, and they denied it, he served them as enemies. Whence, if a small party may with God's approbation deliver themselves, and the whole of their community, from the bondage of their oppressing dominators whom they had served several years, and may punish their princes that do not come out to their help, in a concurrence with them, and encouragement of them in that attempt; then must it be duty to defend themselves against their oppressors that rule over them, and all ought to concur in it; or else there would not be justice in punishing them that were defective in this work; but we see the former from this example: therefore,—Obj. If it be said, Gideon, and the rest of the extraordinary raised judges, were magistrates, therefore they might defend and deliver their country, which a private people that are only subjects may not do. I answer. (1.) They were subject to these tyrants that oppressed them who were then the sovereign powers of that time, and yet they shook off their yoke by defensive arms. (2.) They were not then magistrates when they first appeared for their country's defence and deliverance, neither in that did they act as such, but only as captains of rebels, in the esteem of them that had power over them. It is clear, Gideon was not ruler, till that authority was conferred upon him after the deliverance. See Judg. viii. 22, &c. yet he did all this before.
When his bastard Abimelech usurped the government, and was made king by the men of Shechem, at length God sending an evil spirit between him and his accomplices that set him up, not only was he resisted by the treacherous Schechemites, (which was their brand and bane in the righteous judgment of God), for their aiding him at first and killing his brethren, Judg. ix. 23, 24, &c. but also he was opposed by others of the men of Israel, as at Thebez, where he was slain by a woman, vers. 50. at the end. Whence, if an usurping tyrant, acknowledged as king by the generality, may be disowned by the godly, and threatened with God's vengeance to consume both him and his accomplices that comply with him; and if he may be opposed and resisted, not only by those that set him up, but also by others that were in subjection to him, and at length be killed by them, without resentment of the rest of the nation; then must it be duty for a people, who had no hand in the erection of such a dominator, to defend themselves against his force; but the former is true by this example: therefore——.
5. When Israel fell under the tyranny of Ammon, oppressing them eighteen years, they did, by resisting these supreme powers, shake off their yoke, under the conduct of Jephthah. And being challenged sharply by the men of Ephraim, who it seems claimed the prerogative of making war, and therefore came to revenge and reduce Jephthah and his company to order, casting herein belike a copy to our regular loyalists, who are very tenacious of this plea of the Ephraimites, that, at least, without the nobles of the kingdom, no war is to be made; yet we find Jephthah did not much regard it, but stoutly defended himself, and slew of them 42,000 men, by their Shibboleth, Judg. xii. If people then, when questioned for defending themselves, by them that claim a superiority over them, and should deliver them, may defend themselves both without them and against them; then it is a people's duty and privilege: but the former is true by this example.
6. They were then made subject to the Philistines 46 years, whom the men of Judah acknowledged for their rulers: yet Samson, that rackle-handed saint, never ceased from pelting them upon all occasions: and when challenged for it by the men of Judah, saying, 'Knowest thou not that the Philistines are rulers over us? What is that, that thou hast done?' Samson objects nothing against their being rulers; but notwithstanding prosecutes his purpose of vindicating himself in defence of his country, as they did unto me, says he, so have I done unto them, Judg. xv. 11. Hence, If saints may avenge themselves upon them whom the country calls rulers, and when enabled by God, may do to them as they did to them; then must it be a duty for them to defend themselves against them; but the antecedent is true by this example.
7. When Saul, in the pursuit of the Philistines, had charged the people with a foolish oath (like unto many of the ensnaring oaths that monarchs use to impose upon people) not to eat any food until the evening, Jonathan his son tasted but a little honey, and lo he must die; which Saul confirmed with another peremptory oath, God do so to him, and more also, if he should not die. Whereupon the people, as resolute on the other hand to save him, resisted the rage of that ruler, and swore as peremptorily, that not one hair of his head should fall to the ground. So the people rescued Jonathan that he died not, 1 Sam. xiv. 44, 45. Hence, If people may covenant by oath to resist the commands, and rescue a man from a tyrant's cruelty, then it is duty to defend themselves against him: the antecedent is true here.
8. Afterwards, when the manner of the king, presaged by Samuel, was verified in Saul's degeneration into many abuses of government, this privilege of resistance was not wholly mancipated, but maintained by David's defensive appearance with his little army, he took Goliah's sword, not for ornament, or only to fright Saul, but to defend himself with it, and was captain first to four hundred men, 1 Sam. xxii. 2. had a mind to keep out Keilah against him with six hundred men, 1 Sam. xxiii. 13. and afterwards a great host came to him to Ziklag, while he kept himself close because of Saul the son of Kish, 1 Chron. xii. 1. throughout, where they left Saul, and came and helped David against him. This is proved at length by Lex Rex. quest. 32. p. 340.
9. The city Abel, whether Sheba the traitor had fled, did well to resist Joab the king's general, coming to destroy a whole city for a traitor's sake, and not offering peace to it (according to the law, Deut. xx. 10.) and defended themselves by gates and walls, notwithstanding he had a commission from the king, 2 Sam. xx. and after the capitulating, they are never challenged for rebellion.