In modern theology, John’s Gospel is often used to speak about the theology of the perichoresis of the Trinity. Most of the blame for this can be put on Jurgen Moltmann, who interpreted John 17:21, “as you Father, are in me and I in you,” to speak of “the inner life of the triune God.” It can be pointed out that this verse in particular, and all of the Gospel of John in general, never speaks of the Father or the Son being in the Spirit, or the Spirit being in the Father or the Son. While the Gospel of John later became very important for defining Trinitarian theology, it is anachronistic to read these later ideas back into the text, making the text say something which it flatly does not.
The perichoretic relationship between the Father and the Son in the Gospel of John is immediately apparent. The Son is “in the bosom of the Father” (1:18), Jesus says that “the Father is in me and I am in the Father” (10:38), again “I am in the Father and the Father is in me” (14:10-11), and the verse above from 17:21. While one can get the sense from these verses that this relationship is mutual between two equals, one must also keep in mind verses such as 14:28 where Jesus says “The Father is greater than I” and other verses that show a dependency of the Son upon the Father such as 5:26 and 6:57. The Holy Spirit fits into this relationship only twice. John 1:32 describes the Spirit as a dove which remained on Jesus, though this identification is somewhat unwieldy since verse 33 says that the one who this Spirit remains on is “the one who baptizes with the Holy Spirit.” The second example, John 3:34, is also cryptic. In this verse the Spirit is given, though it is unclear if the Spirit is given by God or by the one whom God has sent.
From this evidence it can be seen that the Spirit is not described in the same terms as the Father and the Son. In the Gospel of John the Spirit is described as an agent of the Father and the Son. John 14:16 calls the Spirit “another Counselor” who is given by the Father. John 15:26 says that this Counselor is sent by the Son from the Father and proceeding from the Father. And in John 16:7 Jesus says that he will send the Counselor. Even with this inconsistency of where the Spirit is coming from, there is a consistency in whom the Spirit is given to, the disciples.
The disciples are described very uniquely in the Johannine literature as having a relationship with the Father and the Son that is very similar to the relationship that the Father and Son have with each other. Indeed, it may even be suggested that for John the triune perichoresis consists of not the Father, Son, and Spirit but the Father, Son, and disciples. The clearest example of this is John 14:20 where Jesus says “On that day you will know that I am in my Father, and you in me, and I in you” and 17:21 “As you, Father, are in me and I am in you, may they also be in us.” The disciples are in the Son and the Son in the disciples when they “eat my flesh and drink my blood” (6:56). The disciples are called to “Abide in me as I abide in you” (15:4) like branches to a vine. Also, the Son seeks that himself, and the love he has from the Father, may be in the disciples (17:26). In 1 John this language of “abiding in” is placed within the context of obedience. 1 John 2:6 warns, “Whoever says, ‘I abide in him,’ ought to walk just as he walked.” And again in 1 John 3:23 “All those who obey his commandments abide in him, and he abides in them.” But in 1 John 4:15 this is dependent upon a confession of faith, “God abides in those who confess that Jesus is the Son of God.” And in 1 John 2:24 “If what you have heard from the beginning abides in you, then you will abide in the Son and in the Father.” Though in 1 John 5:20 it is simply “we are in him who is true, in his Son Jesus Christ.”
Though the disciples are put into a perichoretic relationship with the Father and the Son, one must not mistake this as saying that the disciples are elevated to the divine in Johannine theology. Rather, the disciples have this perichoresis precisely through the Holy Spirit, “And by this we know that he abides in us, by the Spirit that he has given us” (1 John 3:23), and “By this we know that we abide in him and he in us, because he has given us of his Spirit (1 John 4:13). How this is accomplished in Johannine theology is a bit of a matter of debate. In the Gospel of John there is a double giving of the Holy Spirit. In John 20:21-22 Jesus breaths on his disciples instructing them to “receive the Holy Spirit.” In John 19:30, however, Jesus also “hands over” the Spirit. The relationship between these two events, if there is recognized to be a relationship at all, is unclear. If one takes John 16:7 literally when it says “if I go, I will send him [the Counselor] to you” then when Jesus “goes” by his death on the cross is also when the Spirit is “sent” into the world. Then in John 20:21-22 is when Jesus bestows this Spirit, who is now come into the world, specifically upon the disciples. In 1 John 2:20-27 we see the continuation of this bestowal of the Spirit in proto-chrismatic language. Those belonging to God have been “anointed (chisma) by the Holy One” (2:20) and “the anointing that you received from him abides in you” (2:27). Though this anointing the “little children” have knowledge (2:20) and are taught the truth (2:27), just as the Spirit is described as the guide “into all the truth” (John 16:13) and the “Spirit of truth” (John 14:16 and 15:26).
A few interesting points can be gleaned from these verses. First, the disciples are said to abide first of all in the Son. Only through the Son are the disciples spoken of abiding on the Father. Also, unlike the Father and the Son who have their perichoresis as an essence of their being, the disciples must continue to abide in the Son through their continued obedience. In other words, the perichoretic relationship of the disciples with the Son is purely volitional. Finally, the Spirit is primarily the agent by which the disciples enter into this perichoretic relationship with the Father and the Son. Through the Spirit the disciple moves from darkness to light (John 3:5-8, 6:63), is transformed into a worshipper of God (4:23-24) and gains victory over sin (1 John 3:9). Therefore, it is through the Spirit that the disciple comes into eternal life (1 John 5:20).
In conclusion, we can see that nowhere in Johannine literature is the Spirit spoken of as having a triune perichoretic relationship with the Father and the Son. Rather, the Spirit only comes into this relationship by its indwelling in the disciples, who then, through the Spirit’s help, come to abide in the Son and through the Son the Father as well. Therefore, while it can be said that the Johannine literature does not have a very strong Trinitarian theology when it comes to speaking of the Trinity as three separate and independent beings who have an eternal triune inner life, from examining the role the Spirit has in the disciples, and the relationship of the disciples with the Son, we can see that the Spirit is, in fact, integrally connected to the Father and the Son. This suggests then that for Johannine Literature the Trinity was did not necessarily consist of three separate and intradependent beings, but that the Father, Son, and Spirit consist of how they work in and through the disciples.
 References are from David Crump, “Re-examining the Johannine Trinity: perichoresis or deification?” Scottish Journal of Theology 59:4 (2006) 395-412. This paper is based upon, though also diverges from, this article.