“As God, the Son is omnipresent in his divine essence. As man, the same Son is present in just one place at a time, now at the right hand of God the Father (Heb. 1:3). In his speech in Acts 7 Stephen defends himself from the charge that he denounced the temple.
He does not deny that the temple was the dwelling place of God, but he does recount various ways in which God had met his people in other places before and beyond the temple, even on Gentile ground in Mesopotamia, Egypt, and the wilderness.
Toward the end of his speech Stephen sees heaven itself opened and Christ standing at the right hand of the Father. He is the new temple (John 2:18–22), the dwelling place of God, now in the heavenly home of God’s glory. There is a new place where God dwells, and it is in the heavenly Jesus.
Given this, how could Jesus himself promise his disciples, “I am with you always, to the end of the age” (Matt. 28:20)? If he is in heaven, and heaven is the place of glory, how can he be with us here below in the goodness and grace of his human nature?
John Calvin puts the answer beautifully: “The coming of the Spirit and the ascent of Christ are antithetical.” When Christ ascends, he sends the Holy Spirit down to be with us.
Because the Spirit is his Spirit, the Spirit of Christ (Rom. 8:9), he mediates Christ’s presence to us. The Son is with us to the end of the age by the Spirit.
Does this then mean that we always have our Brother with us, but not our Father? Do we have only the goodness and grace of the Son with us but not the goodness and grace of the Father?
Is God the Father ever-present with us only in his essence (as he is present even to the lost), but not as our loving Father? This does not follow, because as the Son is present in his goodness and grace by the Spirit, so the Father is present in his goodness and grace by the Son.
The Spirit makes the Son present to us, and in doing that makes the Father present to us as well, because the Father is in the Son, and the Son is in the Father (John 14:10).
The persons of the Godhead indwell one another, so that by having the Son in us by the Spirit, we have the Father in us by the Son.
Our Brother and Father together come to dwell in us: “If anyone loves me, he will keep my word, and my Father will love him, and we will come to him and make our home with him” (John 14:23).
Because the Son has promised us that he will never leave, we have the same assurance from the Father, who is in him.”
–Garry J. Williams, His Love Endures Forever: Reflections on the Immeasurable Love of God (Wheaton, IL: Crossway, 2016), 90–91.