Thank you for your question. There are several parts to it, so let me try to go through some of them.
First of all we can be thankful that the Lord Jesus Christ prayed for the unity of the church, otherwise, given man's sinfulness, there would never be any hope for us! But in John 17 Christ, interceding for the church, prayed that all his people may be one. Has the Father heard and answered Christ's prayer?
We have to say that the Father has both answered and will answer his Son's prayer. There will be a great, final display of unity before the throne of God which the book of Revelation anticipates in chapter 7:9. No divisions of any kind will remain in that because all sin will be removed and every Christian will know even as he is known as the truth of Christ's glory and of heaven itself will be completely clear. So Christ's prayer for the church will be fully answered in eternity.
Here below, however, it is true that we see many divisions. There are certainly divisions between those who believe the Scriptures to be God's inspired Word and those who don't. There can't be unity when there is such basic disagreement about who God is, who Christ is, what is sin, how we are saved, and so on. Lies and truth cannot co-exist. That explains some divisions.
There are other divisions that are the result of different interpretations of Scripture. Some Christians practice credo-baptism, the baptism of only those who can make a credible profession of faith. Reformed Baptists would say that. Others, like the Orthodox Presbyterian Church, believe the Bible teaches that God is at work in the covenant to call families to himself and to work through the normal means of parental training to bring children up in the nurture and admonition of the Lord, so that children do rightfully belong in the church as baptized members because they are part of the covenant. There are also divisions over the kind of church government which is biblical and proper. Congregationalist churches believe that each congregation exists separately unto itself while Presbyterians believe that Scripture teaches that churches are connected to one another.
There are divisions because of history and circumstance. Some Reformed churches developed in Germany or in the Netherlands, others developed in Scotland and Ireland or France. Often there is an easy going back and forth between those churches because they each have very similar and their view of the church is very similar. Here is what the Westminster Confession of Faith (chapter 25) says about the church:
Chapter 25, Of the Church
1. The catholic or universal church, which is invisible, consists of the whole number of the elect, that have been, are, or shall be gathered into one, under Christ the Head thereof; and is the spouse, the body, the fullness of him that filleth all in all.
2. The visible church, which is also catholic or universal under the gospel (not confined to one nation, as before under the law), consists of all those throughout the world that profess the true religion; and of their children: and is the kingdom of the Lord Jesus Christ, the house and family of God, out of which there is no ordinary possibility of salvation.
3. Unto this catholic visible church Christ hath given the ministry, oracles, and ordinances of God, for the gathering and perfecting of the saints, in this life, to the end of the world: and doth, by his own presence and Spirit, according to his promise, make them effectual thereunto.
4. This catholic church hath been sometimes more, sometimes less visible. And particular churches, which are members thereof, are more or less pure, according as the doctrine of the gospel is taught and embraced, ordinances administered, and public worship performed more or less purely in them.
5. The purest churches under heaven are subject both to mixture and error; and some have so degenerated, as to become no churches of Christ, but synagogues of Satan. Nevertheless, there shall be always a church on earth, to worship God according to his will.
6. There is no other head of the church but the Lord Jesus Christ. Nor can the pope of Rome, in any sense, be head thereof."
There is real and active unity around the truth. Untruth can never bring unity, but truth always should. Whether or not we see organic, actual, visible unity among the churches, even among Reformed churches, Christ's prayer is being answered when I receive another brother or sister because they confess the same Lord and Savior I do. I have fellowship with them even as we might disagree about baptism or church government or even whether they believe that Jesus Christ died for those whom the Father gave him alone. If they have their hope in Christ to save them from their sins, we have a place to start in building our unity of the faith in the bond of peace (Eph. 4:1ff). I encourage you to start with the truth of the gospel and begin to work out from there, not letting disagreements with other believers over doctrine (unless their beliefs are against what the Bible teaches!) keep you are seeing the unity that the truth of God's Word can and does bring.
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