In the midst of all the trials and difficulties Christians experience in a hostile world, Christ’s plea for His disciples is that they would be one. He prays, “Holy Father, keep through Your name those whom You have given Me, that they may be one as we are one” (John 17:11; NKJV). He comes back to this theme a little later in His prayer. “I do not pray for these alone, but also for those who will believe in Me through their word; that they all may be one, as You Father, are in Me, and I in You, that they also may be one in Us, that the world may believe that You sent Me” (vv. 20,21).
First of all, it should be noted that Jesus makes a distinction between believers and unbelievers, and He makes it clear that He is not praying here for unbelievers. He prays “for those who will believe in Me.” The phrase translated “believe in” is used throughout the Gospel of John to refer to personal faith in Christ. What He is praying for here is the unity of a fellowship of believers – not a state church or a church with liberal theology. And Jesus made it clear in verse 9 that “I pray for them. I do not pray for the world but for those whom You have given Me, for they are Yours.” He draws a sharp distinction between the world and true believers. He is praying for the unity of genuine born-again Christians, not a mixed body of converted and unconverted church members. It is a believers’ church that is in view here.
On the other hand Jesus makes it plain that He is praying for all genuinely born again Christians. “I do not pray for these alone [i.e., His immediate disciples], but also for those who will believer in Me through their word” (v. 20). His concern is not just for one particular denomination or sect, but for the universal church as a whole – all who genuinely believe in Him in every age.
Jesus describes the nature of church unity this way: “as You, Father, are in me, and I in You; that they also may be one in us” (v. 21). “I in them, and You in Me, that they may be perfect in one” (v. 23). There is a certain amount of mystery here, the nature of the Godhead and the manner in which the Father is in the Son and the Son in the Father. But it does point to what theologians call the mystical union of believers in Christ. If we have been born again we have the Holy Spirit dwelling in our hearts; and this connects us mystically to Jesus Christ and to each other. All true believers have the indwelling of the Holy Spirit. We are all members of the body of Christ, regardless of our particular denominational affiliation. We all share a common connection to Christ. He is the head of the one universal church of which we are all members. Thus every truly born-again Christian is a brother or sister in Christ.
It is for this church, this universal church, that Jesus prays “that they all may be one . . .” (vv. 21-23). He prays that they might be one, not many.
Here we see the great scandal of modern American church life. We are a nation made up of ethnic groups from every corner of the globe. We enjoy the freedom of religion, the separation of church and state. Unfortunately that has resulted in an incredible array of denominations. There are at least six or sever conservative Presbyterian groups alone, each claiming to subscribe to the Westminster Confession of Faith. Much to our shame we have come to accept this as normal. Churches feel free to define themselves any way they wish, often putting highly debatable doctrines in their statements of faith, and then requiring their candidates for membership to subscribe to the statement of faith in full. Individual Christians simply shop around and choose whatever church they wish to join, sometimes changing membership repeatedly from church to church.
Some of the more conservative or “Fundamentalist” churches practice what is called “Second Degree Separation.” “First Degree Separation,” separation from unbelievers, is biblical. Evangelical Christians should not be part of liberal, mainline denominations that deny the cardinal doctrines of the faith. That would be tacitly recognizing unbelievers as brothers and sisters in Christ. But “Second Degree Separation,” separation from fellow Evangelical Christians over secondary points of doctrine, is problematic. If we are to take Jesus’ words in this prayer seriously, we should all be working for the visible unity of the church.