“The Spirit’s coming inaugurates a communion with Christ in which the Spirit who dwelt on Christ now dwells on and in believers… The coming of the Spirit is the equivalent of the indwelling of Jesus…
Having the Spirit is the equivalent, indeed the very mode, of having the incarnate, obedient, crucified, resurrected and exalted Christ indwelling us so that we are united to Him as He is united to the Father.
It is this sense that John sees the difference that Pentecost signals in the ministry of the Spirit. Now, as the bond of union to God, the Spirit indwells all who believe as the Spirit of the Lord Jesus Christ. This is a development of epochal proportions.
The Spirit who was present and active at Christ’s conception as the head of the new creation, by whom He was anointed at baptism (John 1:32-34), who directed Him throughout His temptations (Matthew 4:1), empowered Him in His miracles (Luke 11:20), energized Him in His sacrifice (Hebrews 9:14), and vindicated Him in His resurrection (1 Timothy 3:16; Romans 1:4), now indwells disciples in this specific identity.
This is the meaning of our Lord’s words, otherwise impossible to comprehend: ‘It is for your good that I am going away’ (John 16:7).”
–Sinclair Ferguson, The Holy Spirit: Contours of Christian Theology (Downers Grove, IL: InterVarsity Press, 1996), 71-72.