25 O righteous Father, the world hath not known thee: but I have known thee, and these have known that thou hast sent me.
26 And I have declared unto them thy name, and will declare it: that the love wherewith thou hast loved me may be in them, and I in them. (John 17:25–26)
Why did Jesus in the latter part of John 17 pray that He would be “in” His disciples? Is this something different from having the Holy Spirit indwell them?
Previous to His prayer in John 17 the Lord had prepared His apostles for His impending departure back to the Father by not only informing them about it, but by especially informing them about the provisions that they would soon receive in order to be able to successfully function in His absence during the final stage in God’s program with Israel. And in connection with doing so, the Lord had particularly said to them,…
16 And I will pray the Father, and he shall give you another Comforter, that he may abide with you for ever;
17 Even the Spirit of truth; whom the world cannot receive, because it seeth him not, neither knoweth him: but ye know him; for he dwelleth with you, and shall be in you.
18 I will not leave you comfortless: I will come to you.
19 Yet a little while, and the world seeth me no more; but ye see me: because I live, ye shall live also.
20 At that day ye shall know that I am in my Father, and ye in me, and I in you. (John 14:16–20)
So then when the Lord prays to the Father in John 17, He specifically fulfills this promise that He had made to “pray the Father” for them.
Now as the Lord had said to them in John 14, one of the particular issues about which He would “pray the Father” was the issue of them not being left “comfortless” in His absence. Rather, as He said, “I will come to you.” And as He explains throughout John 14–16, this would be accomplished by the ministry of “the Holy Ghost” being sent to them. In accordance not only with the unique capacity of the Holy Ghost, but also in accordance with what the Lord says to His apostles about His special ministry to them, the Holy Ghost Himself would be the mechanical means by which the Lord would both “come” to them and be “in” them. Hence the Lord said to them that when they were given the Holy Ghost, “At that day ye shall know that I am in my Father, and ye in me, and I in you.”
Therefore it is by the person and ministry of the Holy Ghost that both the Lord and the Father would be “in” the apostles, as per the Lord’s doctrine to them in John 14–16 and in accordance with the Lord’s prayer for them in John 17.
Likewise with us in this present dispensation of God’s grace it is by the person and ministry of the Holy Ghost that the Lord lives in us in accordance with God’s program with us. Hence, for example, the apostle Paul calls the Holy Ghost “the Spirit of Christ.”
– K.R. Blades