And the Spirit was sent by the Son to indwell believers after the Son ascended to Heaven after His resurrection (Jn. 16:7).
Those truths are (generally) affirmed by all believers today. Yet there is much confusion today about just how the Spirit relates to believers. Specifically, what is the nature of His indwelling, baptism, and filling?
Every believer can rest in the fact that the Spirit has regenerated him. It is the work of God’s Spirit to produce new life in the believer (Tt. 3:5). It is thus the Spirit of God that produces salvation in the believer. And following that salvation, the Spirit immediately indwells every believer (1 Cor. 3:16; 6:19; 2 Cor. 5:5). If one is a believer, he can be sure that the Spirit of God resides in him. That never changes for any believer.
And not only does the Spirit indwell every believer, but the Spirit also baptizes every believer into union with Christ (1 Cor. 12:13). This is often misunderstood as some separate act of the Spirit that happens subsequent to salvation. But Paul is clear that in the act of baptism, the believer is united to the work of Christ in His death, burial, and resurrection (Rom. 6:4). This is true of every believer.
What is not true of every believer though, is that not every believer is always filled with the Holy Spirit. While filling is often misunderstood, it is simply explained as being under the control of the Holy Spirit. The believer who is filled with the Spirit is submissive and obedient to the Holy Spirit. Notice also that Paul is clear in Ephesians 5:18ff that this filling or control is recurrent (not continual) and dependent on the obedience of the believer. In other words, every believer can be filled with the Spirit at any time, but not every believer will always be filled with (controlled by) the Holy Spirit. In fact, any time a believer is in willful disobedience to the Spirit, it is clear that he is not — and cannot be — filled by the Spirit at that time.
So putting this together, we can clearly say that every believer is always indwelt by and baptized by the Spirit, though he may not always be filled by the Spirit. Or said another way, even when a believer is not filled by and under the control of the Spirit, he is still always indwelt by the Spirit and identified with Christ through baptism.