“The glory of God entered into the tabernacle and temple of old in clouds and darkness; but the glory of God enters into the gospel church, under the New Testament, in light.
Christ hath promised to be with His church to the end and consummation of all things.
Christ is thus present with His church, principally and fundamentally, by His Spirit. There are three ways of the presence of Christ:
1. He is everywhere essentially present; present with all things by the immensity of His divine nature. Christ did not promise this, for it is not a subject for a promise. The promises are of what may be, and not of what cannot but be.
This presence is necessary, and cannot be otherwise; neither doth it make any alteration. It doth not make a church; it doth not make one place heaven, another hell. I speak of the immense presence of the divine nature.
2. Christ is, or may be, present in His human nature: this was that which brought a great entanglement on the spirits of His disciples. He told them He would never leave them; and where but two or three of them were assembled in His name, He would be among them, Matt. 18:20.
At length He comes and tells them, “It is expedient for you that I go away,” John 16:7.
This filled their hearts with trouble; they knew not how to reconcile these things. Afterward, they were told that He was so gone from them as that they must not look for Him till the day of judgment, Acts 3:21.
3. There must be, therefore, some other presence of Christ besides the essential presence of his divine nature, and besides the presence of His human nature; how else shall the promise be accomplished? Saith Christ:
“I will tell you what that presence is; I will send you the Holy Ghost, to supply the presence of my human nature.”
It is the substance of the 14th, 15th, and 16th chapters of John, to declare this.
“I will send you the Comforter to abide with you, to enable you to all church work. Therefore, though I am with you, and have instructed you, yet you can perform no church work at all, until the Holy Ghost comes. Abide at Jerusalem, till you have the promise of the Spirit.”
After the ascension of Christ, the apostles went about no church work till they had received the Holy Ghost.
And Christ hath no vicar, but the Spirit.
The truth is, the world grew weary of Him, and took the work out of His hands for which He was promised; and He would have nothing to do in that which they call “the church.”
I need not prove this; it hath been the faith of the catholic church, from the first foundation of it, that the promised presence of Christ with His church was by His Spirit.”
–John Owen, “Sermons to the Church ,” The Works of John Owen, Volume 9 (Carlisle, PA: Banner of Truth, 1684/2000), 9: 443-444.

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