The "Mystery of the Church" is the title used by the Second Vatican Council to aptly introduce its teaching about the Church. A "mystery" is a revealed truth, a reality pertaining to the realm of faith, which we can know and understand only because God's word has revealed it (the human mind by itself cannot do so). Hence, a "mystery" is something to be experienced by the heart, rather than be fully understood by the mind. Also, what is revealed is an ideal, which in practice requires our committed cooperation to become what God intends it to be.
All the mysteries of faith are necessarily interconnected. The first mystery (or revealed truth) is that God created us in his own image and likeness (this means that he let us share in his own qualities of heart and mind: "freedom to love" and "intelligence"). God then invited human beings to "a divine-human partnership", mandating men and women to multiply and fill the earth, and to subdue it and rule it.
The second "mystery" is that God did not change this plan even though mankind sinned, and fell into the clutches of another mystery, called "Evil". Continuing to "so love the world", God sent his only Son, Jesus, to continue this partnership in a most perfect way, and so to become a Model for humanity in its efforts at overcoming Evil.
Gradually, more "mysteries" were revealed, the Incarnation, the Cross, the "Church", etc.
Wanting, even after his death and resurrection, to continue the "incarnational method of salvation", Jesus established the Church to be his own Body (1Cor.12:27), of which He would be "the Head" (Col.1:18). He gave spiritual authority to it (Mt.16:19). Sending the Holy Spirit to give birth to this Church on Pentecost Sunday, Jesus fulfilled his promise, "You are Peter, and on this rock I will build my church, and the powers of death shall not prevail against it" (Mt.16:18).
1. This church is the Roman Catholic Church, for Peter (and Paul) went to Rome from Jerusalem, and were martyred there, with the early Christians. So too were many "popes", the successors of Peter as the "bishop of Rome". And because there is an unbroken line of apostolic successors from Peter to our present Pope John Paul II, the statement of belief of the People of God (Nicene Creed) calls this Church "one, holy, catholic and apostolic".
It was not easy to remain "one"! For 2000 years, the powers and lords of this world used every means to destroy the Church, as it spread to every country of the world. There were also crises and tensions within the Church, regarding relationships and doctrine. Still, the power of the Holy Spirit kept the vast majority of bishops and believers united under the Pope, fulfilling the words of Jesus, "the rain fell and the floods came and the winds blew and beat upon that house, but it did not fall, because it had been founded on the rock!" (Mt.7:25). This Church today has about one billion members who belong to different litugical rites (Latin, Syro-Malabar/Malankara, Maronite, Coptic, etc.) but are all united in doctrine and in obedience to the Pope.
The vitality and dynamism of this Church is seen in its unceasing and multifarious activity for the sake of the Kingdom of God. In the fields of culture, art, music, literature, education, the sciences, international relations, peace and development, etc; in its vast missionary activity; in its faithful preservation and proclamation of the Bible and the fostering of biblical studies; in its encouraging the life of prayer, both among religious and the laity; in working for the poor and oppressed in innumerable works of charity as well as of social justice - in all of these and more, the efforts of the Catholic Church have been unsurpassed, winning the admiration even of its enemies.
2. What about the other churches which came into being later? In the early centuries, two major centres of Christianity had been developing, one in the Eastern part of the Roman Empire, located in and around Constantinople and with a Patriarch as the head (the Byzantine Church), and the other in the Western part of the Roman Empire, located in and around Rome, with the Pope as the head (the Latin Church). Both were in full communion with each other (as regards sacramental life and doctrine), and the primacy of the Pope was accepted by the Patriarch. Seven Ecumenical Councils were held in common (from 325-787) to define the doctrine ("dogmas") of Christianity.
Gradually however, for political rather than religious reasons, the two got more and more estranged, and in 1054 AD the Pope's Legate excommunicated the Patriarch in Constantinople. Thus, the first major split in Christianity took place. The current membership of the "Orthodox" or Eastern Churches is about 200 million. "These Churches, though separated from us, yet possess true sacraments, above all - by apostolic succession - the priesthood and the Eucharist, whereby they are still joined to us in closest intimacy" (Vatican II's Decree on Ecumenism).
The next major split took place 500 years later, giving rise to the "Protestant" Churches (from 1527 onwards) and led by Luther, Zwingli, Calvin, and finally King Henry VIII. It is claimed that one reason for Luther's revolt was to protest the immorality and greed among the clergy, but this was more the occasion than the cause. Luther's main protest was about doctrine, for he believed that the Holy Spirit had given him alone the right understanding of the saving doctrine of Christ. As for the Anglicans, Henry VIII of England was furious with the Pope for not allowing him to divorce his wife and marry another woman, so he broke with Rome and made himself the head of the Church of England.
The Protestant Churches (Lutheran, Methodist, Episcopalian, Baptist, etc) today have about 250 million members, and they differ from us in that they have no priesthood, or apostolic succession, and do not accept "both scripture and tradition", but go by the principle "scripture alone", and do not favour Marian devotion, prayer to the saints, etc.
The most recent major split has taken place in this century (from 1901 AD) giving rise to what are called the "Pentecostal" assemblies (not a Church, since they have no structures of authority, common doctrine, etc). Numbering perhaps 300 million believers, they insist only on what they call "the baptism of the Holy Spirit" and its physical manifestations.
3. From the above, we can see why the Church is a "mystery" - God wills "to unite all things in Christ" (Eph.1:10), but our cooperation is needed for this divine-human partnership! Where the Holy Spirit finds loving and intelligent human cooperation, the story of Christianity is wonderful and praiseworthy. But where the "father of lies" or "Deceiver" succeeds in influencing our human cooperation, the story of God's People becomes soiled and sad.
When will the Churches finally be united, and Jesus' prayer for Unity (Jn.17) be perfectly answered? The Second Vatican Council points first to the need for "interior conversion. For it is from newness of attitudes of mind, from self-denial and unstinted love, that desires of unity take their rise and develop in a mature way." It also "urges the faithful to abstain from any frivolous or imprudent zeal, for these can cause harm to true progress towards unity. Their ecumenical activity must be fully and sincerely Catholic, loyal to the truth we have received from the Apostles and Fathers, and in harmony with the faith which the Catholic Church has always professed..."
As we turn to the Lord in intercession, and seek to cooperate better as partners, He will continue to build "a Church founded on Rock". Already much progress has been made towards unity, with a recent Lutheran-Catholic agreement on "justification by grace alone, to be received by faith, which in turn must be expressed in good works", Anglican-Catholic agreement on "the primacy of the Pope for the sake of the unity of the Body of Christ", etc., etc. It is our hope and our prayer that as the First Millenium saw the Church united, but the Second Millenium saw the Church divided, so the Third Millenium will again see the Church united, by the action of the Spirit and our cooperation. Rejoice, a new springtime is coming for Christianity, and through it new power for evangelising the whole world, Alleluia!