He goes on to elaborate on what this means.
I hold to the sovereignty of God, and also to the free-agency of man, and whilst I believe that God worketh all things after the counsel of his own will, yet it is in such a way as "thereby neither is God the author of sin; nor is violence done to the freedom of the creature; nor is the liberty or contingency of second causes taken away, but rather established." It may not be possible for me to discriminate between the human and the divine agency; nor can I tell where one colour in the rainbow terminates, and where another begins; yet do I know that these colours are different, and both in the rainbow! I may not be able to reconcile the free-agency of man with the fixed purposes of God which I believe; nor can I reconcile the free-agency of man with the foreknowledge of God, which all must believe; suffice it to know that both doctrines are taught in the Bible, and I know that the Bible is true. Do I trample upon reason? I deny it — I have a syllogism. It is this. My heavenly Father says that these doctrines are all true. My heavenly Father never tells lies, and therefore these doctrines are all true! But can they ever be reconciled or explained? I believe they both can, and will be, when God gives the key! Suppose, for a moment, that you were utterly unacquainted with your twofold existence, as consisting of soul and body. Now, whilst believing yourself to be a simple, and not a compound being, suppose I should say: "You are a mortal man, and must soon die ;" and the next moment should pronounce you an immortal being, and affirm that you can never die, but must live for ever! Would you not say, that I spoke very absurdly, and used very contradictory language? But, should I add, wait a little, and you will have the key, and then all will be plain, and you will see that all is true, and there is no absurdity, no contradiction whatever; methinks you would reply, "No, sir, no key will answer, none can reconcile things so perfectly contradictory, 'mortal,’ and yet at the same time 'immortal!" must die! and yet, will not, cannot die! the thing Is absurd. It cannot be! But when you are let into the secret of your twofold nature — O, now! there is no difficulty at all! Even so, in relation to the sovereignty of God, and the free-agency of man, we find it difficult to reconcile these things now, because the key is wanting. In a future state the key will be given, and then there will be no difficulty at all. In the mean time let us remember, that the Bible is suited to our probationary state. We need our faith tried, as well as any other grace, or virtue. And now our grand inquiry is, What does the Bible teach? for
“This is the judge that ends the strife,
Where wit and reason fail;
My guide to everlasting life,
Through all this gloomy vale.”
That the government of God extends, not only to all things but to all events; not only to all creatures, but to all their actions. In other words, that the providence of God is, in some way or other, concerned with all that is done or transpires on earth, is manifest from very many passages of Scripture. The strongest, I think, are those which assert the providence of God in cases where, least of all, it might have been expected.
Thus, in the 127th Psalm, we find it thus written: "Except the Lord build the house, they labour in vain that build it. Except the Lord keep the city, the watchman waketh but in vain." And again, "The lot is cast into the lap, but the whole disposing thereof, is of the Lord." But there is another passage of Scripture, perhaps, yet more remarkable; inasmuch as it asserts the providence and purpose of God in a case involving sin, dreadtul sin! The passage referred to is found in Acts ii. 23: "Him being delivered by the determinate counsel and foreknowledge of God ye have taken, and by wicked hands have crucified and slain." The crucifixion of Christ, by envious and wicked Jews, was certainly a crime of great magnitude; and yet the apostle Peter tells us expressly that it was " according to the determinate counsel and foreknowledge of God.” The explanation of the matter is simply this: God knowing all things, foreknew what evil passions would be waked up in the bosom of the Jews by the life, and doctrines, and reproofs of our Saviour, and he also knew full well to what a murderous deed those evil passions would lead, if not restrained. For wise and benevolent purposes towards our race, God determined, not to restrain those evil passions, but to leave the Jews, (as of course he justly might) to the freedom of their own will — leave them to act out their own depravity; purposing, as I have said, to overrule the whole matter to the accomplishment of great ends. God was certainly under no obligation to exercise a restraining influence upon those wicked Jews; and if He foreknew what crime they unrestrained would commit, his "foreknowledge had no influence on their fault, which had proved no less certain unforeknown;" hence the apostle Peter, at the very time that he speaks of the crucifixion of Christ as being according to the determinate counsel and foreknowledge of God, nevertheless, charges home all the guilt thereof, upon the wicked Jews. Observe his language! "Him, being delivered by the determinate counsel and foreknowledge of God, ye have taken, and by wicked hands have crucified and slain.”
The case of Joseph also, is precisely in point. He was hated by his brethren, and by them sold into Egypt. This was a great sin; and afterwards, when in trouble, they freely confessed it. "And they said, one to another, we are verily guilty concerning our brother, in that we saw the anguish of his soul, when he besought us, and we would not hear, therefore is this distress upon us. And Reuben answered, saying, Spake I not unto you, saying, Do not sin against the child, and ye would not hear, therefore, behold also, his blood is required." Thus, all who had a hand in selling Joseph, acknowledged, and felt that they had acted freely, and they writhed under the stings of an accusing conscience. Yet, when Joseph made himself known unto them, and they were greatly troubled at his presence, what said Joseph unto them? "I am Joseph, your brother, whom ye sold into Egypt. Now, therefore, be not grieved, nor angry with yourselves, that ye sold me hither; for God did send me before you to preserve life. Ye thought evil against me, but God meant it unto good, to save much people alive." There needs be no difficulty. The case is simply this. God being infinitely wise, knows how, in perfect consistency with the perfections of his character, to make use of all instrumentalities, good and bad, for the accomplishment of his wise and benevolent purposes. Certain things God brings to pass by a positive agency. Other things he simply permits to come to pass. And, let it be remarked, permission and approbation do not, by any means, mean the same thing. Napoleon Bonaparte, when a child, wished to go to a certain place, but was forbidden by his mother. Being headstrong, he persisted in going. "Well, my son," said his mother, "you may go, but remember! it is not with your mother's approbation." And thus God oftentimes permits things which, so far from commanding, he forbids, and highly disapproves. He permits sometimes because he would not interfere with the free-agency of the creature. He permits, sometimes, because he purposes (as in the cases already mentioned) to overrule the evil intended for good; and sometimes he permits, in a judicial way as a punishment for sins previously committed. Hence the language of Paul in reference to the heathen and their abominations: "Even as they did not like to retain God in their knowledge, God gave them aver to do things which are not convenient."
And now let it not be forgotten, this is all that is meant by a certain passage in our Shorter Catechism, which has been much caviled at, viz. "The decrees of God are his eternal purpose, according to the counsel of his will, whereby, for his own glory he hath foreordained whatsoever comes to pass." In other words it may be stated thus: By the decrees of God, we mean no formal legislative enactment, (as, "Thus it shall be," and "thus it shall not be,") but, simply the calm and settled purpose of an infinitely wise and gracious God, to bring to pass; or permit to come to pass whatsoever does come to pass, for the glory of his name. Does any one ask, what is the difference between bringing to pass and permitting to come to pass? I answer, God brought to pass the incarnation of his Son; He permitted to come to pass his crucifixion. The difference is as wide as the east is from the west. Our doctrine, then, is simply this; By positive and permissive decrees, God, in wisdom and in love, manages the affairs of the universe, directs and controls all things, and all events, all creatures, and all their actions. It must be so, for suppose an event to take place without the divine permission; for example, then, it must be either because God is not aware of it, or cannot prevent it. If not aware of it. He cannot be omniscient; if He cannot prevent it, then he is not omnipotent; and then, of course, in the last case, "there must be a power behind the throne greater than the throne itself," which thought would be frightful! No, our doctrine is true, that the government of God extends not only to all things, but to all events, not only to all creatures, but to all their actions. In other words, that a Divine providence is concerned, in some way or other, concerned "in all the good and ill that checker human life."
Is further proof demanded? Permit me to quote a very remarkable passage found in Isaiah xlv. 7; "I form the light, and I create darkness; I make peace and create evil; I, the Lord, do all these things." What! the Lord create evil? Yes! but in such a way as casts no stain upon his moral perfections; but, on the contrary, will furnish new matter for admiration and praise. Hence, the language of joy and gratulation which immediately follows. "Drop down ye heavens from above! and let the skies pour down righteousness. Let the earth open, and let them bring forth salvation. Let righteousness spring up together; I, the Lord, have created it." But how does God create evil. As he does darkness. The first sentence explains the last. Observe the language; I form the light, and I create darkness. How does God form the light? By a positive influence, pouring radiance around How does God create darkness? By withholding this radiance. Even so, by a positive influence, God makes peace, and by withholding that influence, creates evil, that is, permits it. In this, is God the author of sin? No more than the sun is the source of darkness, although its absence occasions that darkness.
Thus, as Baker explains, the Bible teaches — and so does Calvinism — that the sovereignty of God extends to all creatures and their actions in such a way that God is not the author of sin, but overrules all sinful actions to His glory and the good of His people. Read Baker’s full tract on The Sovereignty of God Explained and Vindicated here.