[1.] It is no otherwise the work of the Spirit but as all graces and good works which are in us are His. He “works in us to will and to do of his own good pleasure” (Phil 2:13); He works “all our works in us” (Is 26:12), — “the work of faith with power” (2Thess 1:11; Col 2:12); He causes us to pray, and is a “Spirit of supplication” (Rom 8:26; Zech 12:10); and yet we are exhorted, and are to be exhorted, to all these.
See the contrast Owen is driving at here, even if it's veiled in 17th century English. Every bit of progress in grace that we make -- every single good work which we perform -- are most properly said to be the works of the Spirit. They "are His," as Owen says, and then supports his point by quoting passages that assign very active and causative terms to the Spirit's work in the believers' lives.
Yet having said all that, we, the believers, are rightly exhorted to do all the things that the Scriptures say the Spirit does. We are to want things and do things (i.e., to will and to do) according as it pleases God. We are to perform good works. We are to pray. But it's His work. How does this work?
[2.] The Spirit doth not so work our mortification in us as not to keep it still an act of our obedience.
Read that again. The sovereignty of the Holy Spirit in our lives, even in our progressive, step-by-step, process of sanctification, is not such a sovereignty that it absolves us of responsibility. He is sovereign. He works in us. Yet if we fail to will and to work to God's good pleasure, we have disobeyed. He continues:
The Holy Ghost works in us and upon us, as we are fit to be wrought in and upon; that is, so as to preserve our own liberty and free obedience. He works upon our understandings, wills, consciences, and affections, agreeably to their own natures; he works in us and with us, not against us or without us; so that his assistance is an encouragement as to the facilitating of the work, and no occasion of neglect as to the work itself.
In other words, someone who sits passively by, never lifting a finger -- let alone a sword -- in the faithful fight for holiness in the war against indwelling sin, all in the name of God's grace and sovereignty, is sorely mistaken. The Christian who sits and waits to be zapped with holiness, but never engages in the work of mortification (Rom 8:13), of putting off and putting on (Eph 4:17ff; Col 3:5ff), of making no provision for the flesh in regards to its lusts (Rom 13:14), has prostituted the glorious doctrine of God's absolute sovereignty in the service of his fleshly desires.
But at the same time, see in Owen's words the absolutely gracious ministry of the Holy Spirit. The Spirit, in all the beautiful luster of His sovereignty, doesn't turn us into unfeeling, mindless robots as He works in us to will and to work according to the good pleasure of the Father (no matter how much mileage that caricature has gotten). He doesn't simply force us against our will to obey God. Rather, in unspeakably miraculous sovereignty, He changes our hearts, our affections, our desires, bit by bit, so that when we obey we obey because we want to, because we delight to, because we love to!
Do you see why that's so awesome? It would be easy for God, entirely unfettered by anything in the universe (least of all the will of a mere man), to simply show up and force us to do whatever He wanted. Our hearts and minds would still be corrupt, but we would be "obeying." But that's not how He works. Instead, Christ pours out the Holy Spirit in our hearts, who then opens the eyes of our hearts to see the light of the knowledge of the glory of Christ, who is the image of God (2Cor 4:4). And when our hearts behold that beauty, it is won over, wooed out of its corruption, such that it freely and eagerly follows after that beauty, seeking to get more and more and more it, knowing that more of it comes in the path of obedience. The Spirit is so sovereign, and Christ is so glorious, that our hearts are changed agreeably. Our wills are not violated; they are transformed!
The Spirit works in our hearts and affections, not to present us as unwilling slaves to His wonderful Word, but to begin to see the Word as wonderful, Christ as beautiful, God as glorious, and obedience as satisfying. The Spirit illuminates our lives to have us see things as they are. Sin is devalued and Christ is exalted, and so we follow Him with all our hearts!
And so let us fall on our faces before the Lord God and pray that He would daily pour out His Spirit on us so generously that our affections would be changed, that our eyes would be opened, and that we would love the glory of the preeminent Christ more than the temporal gratification of our own sinful flesh.