In considering what scripture says and what is practiced in the world by professing Christians now and in the past, it is not easy to answer the question in terms of what is observed. As far as what scripture says, even with reference to the messy state of things in that time, it’s not hard. Yes there is clearly one church, even if it takes different forms.
A leading edge crux of the matter seems to be over whether or not we’re talking about a visible or invisible church. I think I prefer to see the church largely in terms of what is visible, for example Spirit baptism and water baptism being so close in the New Testament that even when a passage means at least primarily one or the other, they are never that far apart.
The church based from the Vatican within Rome, called the Roman Catholic Church sees the church as visible. And actually the clearest most straightforward reading of the New Testament text would agree. In fact it is at least somewhat of a strain to come up with an invisible church from the text, unless we see the book of Ephesians pointing in that direction. The Protestant or evangelical emphasis on invisible church is probably not found in scripture. And I don’t think it carries the weight it once did in such circles.
We are left with many different churches, many church denominations which function as the visible church, with the understanding that they are simply part of the church at large. The Roman Catholic Church and the Eastern Orthodox Church each operating separately with renewed calls for reunion carry on what the church has largely understood through most of its history, the oneness of a visible church. Protestant churches and those of both the Reformation and Restorationist (or radical Reformation) seek for one visible church as well, but probably often still mark down divisions to a notion of an invisible church or shrug off differences as not make or break matters.
I am left for the time being with the belief that while there is one true church, it is spread out and at work minus the unity which seems to be an important aspect of what it is. Yes there is definitely unity in the one Lord, the one body through the one Spirit. But visibly it seems to be divided. Not just in the way church is done, but also in some of the interpretations of scripture.
Do we believe God is faithful? Does it depend on us? Just what does scripture mean when it says the church is the pillar and foundation of the truth? In all of the mess God is at work. God continues to work according to his word and promise in Jesus in spite of ourselves and our own lack of understanding in regard to it all. We can rest assured in that.