In my last post, which introduced this series on the reception of the Holy Spirit, I proposed that the New Testament describes two ways that a believer receives the Spirit, which borrowing from biblical language itself I described as the Spirit coming within and the Spirit coming upon. In this post I will list the terms used by New Testament authors that refer exclusively to "the Spirit within" and interpret some of the major passages that talk about this mode of the reception of the Spirit.
The natural place to start is with the terms "the Holy Spirit being/dwelling/remaining in" the believer. The Bible says little about what exactly this is or how it happens (aside from God the Father giving him), but we do know outcomes of the Spirit's indwelling. The Spirit makes the individuals and churches in whom he dwells into temples of God (1 Cor. 3:16; 6:19; Eph. 2:22). Another outcome of the Spirit's indwelling is knowledge of the truth: learning it (John 14:16-17; 1 John 2:27), speaking it (1 Pet. 1:10-11), and guarding it (2 Tim. 1:14). Most importantly, we know that the Holy Spirit dwells in every regenerate believer from a single, but decisive, biblical passage: Romans 8:5-11. According to Paul in Romans, if the Holy Spirit is not in someone, that person thinks and functions according to "the flesh" (which is hostile to God and rebellious against his law), cannot please God, does not belong to Christ, and is headed for death. By contrast, if the Holy Spirit is in someone, that person's spirit is alive, he/she thinks and functions according to the Spirit and is at peace, Christ himself is in that person, and God will eventually raise that person's mortal body from the dead into an immortal body as he did Christ's. In other words, the characteristics and attitude that we expect (and God demands) from a true Christian only belong to the person in whom the Spirit dwells. The person without him cannot possibly be saved. For example, Jude describes false teachers who are destined for eternal damnation in Jude 18-19 as "not having the Spirit."
The Holy Spirit gives new, eternal life to all those in whom he dwells, life of a quality that can't come from any other source. So we see "the Holy Spirit giving life" in John 6:63, "being made alive by means of the Holy Spirit" in Galatians 5:25, and "the Holy Spirit flowing" out of the center of the believer like running (literally, "living") water in John 7:38-39. The imagery of new life continues with the terms "being born of/by/according to the Holy Spirit." Only those who have been born by the Spirit can see and enter the kingdom of God. Only they can recognize each other as kin (John 3:3, 5, 8), and they are misunderstood and persecuted by those who have only been born naturally (i.e., according to the flesh; Gal. 4:23, 28-29).
The indwelling of the Spirit is necessary for God the Father to take ordinary, wicked people and make them into his holy nation. Thus we read of "God choosing [believers] by the sanctification of the Holy Spirit" in 2 Thessalonians 2:13 and 1 Peter 1:2. God chose all believers in the truth to be saved, to obey Christ, and to be cleansed by Christ's blood, which he accomplished by sanctifying them with the Holy Spirit. Likewise believers are "washed by means of the Holy Spirit" by God to be saved by his mercy, regenerated within, declared innocent, sanctified, and made heirs of eternal life (1 Cor. 6:11; Tit. 3:4-7). Of course, until Christ's work on the cross, the Jews assumed that they were and would always be God's holy people and that they were inducted into the people of God by circumcision. But Paul talks about the heart "being circumcised by means of the Holy Spirit," by which any person, Jew or Gentile, becomes a real Jew in God's sight and truly keeps God's law (Rom. 2:29; cf. Col. 2:11-14). Further, it was a given in both Jewish and Gentile thought-worlds that only a holy person could access a divine being in its temple. For a Jew, naturally, that not only entailed being Jewish but for progressively closer access being a Levite or a priest or the high priest himself. But Paul uses the term "having access to the Father by the Spirit" to define the awesome privilege belonging both to all Jews and to all Gentiles through Christ (Eph. 2:18).
Paul repeatedly points out that "having the Holy Spirit" in the present gives believers confidence that God will complete his saving work in the future. All who belong to Christ will receive eternal life in their mortal bodies through the Holy Spirit (Rom. 8:9, 11). The promised resurrection is described as a future redemption, God's purchase of the believers, and indeed, the fact that they have the Holy Spirit already marks them as having been bought with a price (Rom. 8:23; 1 Cor. 6:19-20). Along these very lines, the terms "God giving the Holy Spirit as a pledge [or 'down payment']" and "God sealing [believers] with the Holy Spirit" represent the confidence believers can have of their eventual resurrection because of the Holy Spirit whom God has given them now (2 Cor. 1:21-22; 5:5; Eph. 4:30), a gift closely connected to their faith in the gospel (Eph. 1:13-14).
Another couple of terms remain that pertain to the Spirit within, and they come from one tricky verse, 1 Corinthians 12:13, which reads, "For in one Spirit we were all baptized into one body. Whether Jews or Greeks or slaves or free, we were all made to drink of the one Spirit." Some of the evidence that these terms—"being baptized by means of the Holy Spirit" (which I'll explain shortly) and "the Holy Spirit being given [to believers] to drink"—are connected to the Spirit's indwelling in all believers is the universal scope of the text. Paul insists that we were all baptized into one body by the one Spirit and all made to drink of the one Spirit, and he even gives some examples of opposites according to the flesh (Jew/Greek, slave/free) that are encompassed by the one Spirit's work. (This is reminiscent of the "one baptism" referenced in Eph. 4:5 and "the commonality of the Holy Spirit [my translation]" in 2 Cor. 13:14(13).) It is also notable that Paul made this statement to a church suffering from chronic and severe unity problems, much of which revolved around some people claiming to be more spiritual than the rest because they demonstrated spectacular manifestations of the Spirit that others lacked. Nevertheless, Paul insists that this baptism by means of the Holy Spirit is common to all believers.
Now it would be easy to claim from this passage that "the baptism of the Holy Spirit" is universally received by all believers at conversion as another aspect of the Spirit's indwelling work. But despite the presence of the terms "baptize" and "Holy Spirit" here, this verse does not actually refer to the baptism of the Holy Spirit. The key is the Greek preposition en. In languages in general, prepositions are notorious for being really flexible. (For example, look up "on" in an English dictionary and count the definitions.) In many places, the Greek word en means "in." A pertinent example for our study is Matthew 3:11, which I should introduce by pointing out that the Greek word baptízō, translated "baptize," was actually a run-of-the-mill word meaning "immerse" or "dip": "I [John] baptize/immerse you in [en] water . . . but he [Jesus] will baptize/immerse you in [en] the Holy Spirit and fire." However, another very common meaning of en is "by means of," that is, the tool or instrument that you use to accomplish something. As it happens, the phrase "en the Spirit" occurs several times in 1 Corinthians 12, and in all cases it means "by means of the Holy Spirit." So we see in verse 3, "[N]o one can say, 'Jesus is Lord,' except by [en] the Holy Spirit," and in verse 9, "[T]o another faith [is given by God] by [en] the same Spirit, and to another gifts of healing by [en] the one Spirit." Judging from the pattern of usage Paul already established in this chapter, it is most likely that "in [en] one Spirit we were all baptized into one body" is best rendered "by means of one Spirit we were all baptized into one body." In other words, God the Father used the Holy Spirit to baptize us.
The distinction between "in" and "by means of" is more than grammatical hair-splitting, because it indicates that the baptism Paul mentions here is not necessarily the same as the baptism in/of the Holy Spirit promised by John the Baptist in the Gospels. So what kind of baptism is it? Most likely, Paul is using the metaphor of baptism—which, I again stress, was an ordinary, non-churchy word meaning "immersion," like what you'd do to your dirty pots and pans—like he uses the image of "washing" in 1 Corinthians 6:11 and Titus 3:4-7 mentioned previously, which refers to the removal of sin. This washing/baptism by the Spirit aligns neatly with Paul's description in Romans 6:1-11 of being "baptized into Christ Jesus," which removes sin from us and us from sin, and which is the spiritual reality that physical water-baptism reflects and expresses (and those in sacramental traditions believe enacts). So the physical rite of baptism in water parallels God's action of washing off our sin by the indwelling Holy Spirit when we believe, and so the rite of baptism initiates us all into the visible church in parallel with the indwelling Holy Spirit's work to initiate us into the invisible church composed of those God knows who truly believe.
This work of the Holy Spirit and all his activities listed in this post are performed by the Spirit when he rests within a person, which he begins doing in all genuine, regenerate believers in Jesus Christ at the moment of conversion.