“These words spake Jesus, and lifted up his eyes to heaven, and said, Father, the hour is come; glorify thy Son, that thy Son also may glorify thee: And now I am no more in the world, but these are in the world, and I come to thee. Holy Father, keep through thine own name those whom thou hast given me, that they may be one, as we are. Neither pray I for these alone, but for them also which shall believe on me through their word; That they all may be one; as thou, Father, art in me, and I in thee, that they also may be one in us: that the world may believe that thou hast sent me. And the glory which thou gavest me I have given them; that they may be one, even as we are one: I in them, and thou in me, that they may be made perfect in one; and that the world may know that thou hast sent me, and hast loved them, as thou hast loved me.” John 17: 1, 11, 20-23 KJV
The Church was one for the first thousand years. Now there are over 30,000 different denominations. Since Jesus specifically prayed five times, in this particular passage, that we all be one, it must have been very important to Him and must grieve His heart terribly that we have used our free will to become so separated and fragmented.
I do not see the fragmentation as a bad thing. That's what keeps us challenged to stay true to the teachings of Christ. Too much unity amongst fallible humans tends to lead to all of them following false teachings (in the church) or a deceitful leader (in government). There is one church and she is scattered among many denominations. I think we are facing a time of testing and purification right now. I think there will be a big separation in the church, a reorganization. God is cleaning house. I am not a prophet and I don't speak for God, so that's just based on human observation. But there are some big things happening in churches right now. Big changes. And most are not for the better. A lot of this has to do with weak humans wanting to feel good about themselves and others more than they want to honor and glorify a holy God.