"The grace of our Lord Jesus Christ be with your spirit." Philemon 25
It is the regenerating breath of the Lord Jesus Christ which makes the soul alive unto himself. This is manifest from his own language--"It is the Spirit who quickens; the flesh profits nothing--the words that I speak unto you, they are spirit and they are life" (John 6:63). Then for the first time "the grace of our Lord Jesus Christ is with our spirit." For you will observe that the grace of our Lord Jesus Christ is not with our carnal mind--that ever remains the same, a body of sin and death, flesh--corrupt flesh, "in which dwells no good thing," and therefore not the grace of our Lord Jesus Christ.
His grace is with our spirit, that "new man" of which we read that "it is after the image of God" created in righteousness and true holiness." This is called our "spirit," because it is born of the Spirit, as the Lord himself unfolded the solemn mystery to Nicodemus--"That which is born of the flesh is flesh; and that which is born of the Spirit is spirit." This is no subtle, thinly-drawn distinction, but a very important truth; for unless we see the difference between the two natures, the spirit and the flesh, the law in the members and the law of the mind, we shall always be in bondage, as looking for holiness in the flesh.
The grace of our Lord Jesus Christ being thus with our spirit, it breathes from time to time upon that spirit, moves and acts in it and upon it; for there is what I may call a gracious or spiritual union between the two. Thus we can no more live without the grace of the Lord Jesus Christ than the earth can live without the sun. He must shine, or we have no light; he must revive, or we have no warmth; and he must fertilize, or we bring forth no fruit. Thence time after time there is an outgoing of the single desire of the soul to the Lord Jesus Christ that his grace would be with our spirit; that this grace may be ever flowing forth into us, so as to make us new creatures, dispel all doubt and fear, break to pieces all bonds and fetters, fill us with love and humility, conform us to his suffering image, produce in us every fruit that shall redound to his praise, be with us in life and death, and land us safe in eternity.