Many fundamentalists use Matthew 16 as a prooftext to prop up the idea that the church of Christ has existed continually, without interruption, from the time of Christ until today.
Many will assert that there was no apostasy. They claim a divinely preserved descendency from the Roman Catholic church, as if Catholicism carried the ball for a while and then handed it off to the Reformation, all with no apostasy or deviation from the truth. They say that, "Believers have always existed somewhere. Though we can't tell you their names, we know, by Matthew 16, that the church of Christ has remained continuously on the earth without interruption."
As adherents of Christ's restored gospel, we believe Matthew 16:18 to be the word of God, but we believe that our evangelical friends add more to this passage than the text will support. There is nothing about this passage that guarantees an uninterrupted, continuous succession of Christ's church throughout the ages.
Restorationists maintain that Christ's church will arise and ultimately reign triumphant eschatologically -- as a culmination of history, not as an uninterrupted process over time. The idea being that, in the interim, apostasy is not only possible, but has actually occurred.
Roger Williams founded the first Baptist church in North America. Williams even concluded that the theory of a continuous, uninterrupted succession simply did not make sense. In Liberty of Conscience: Roger Williams in America, Edwin Gaustad conveys Williams' thoughts on this subject:
Christ's appointed apostles, commissioned directly by him, could establish a true church, with true acts of worship, with a congregation of the purified and redeemed. But how, sixteen hundred years later, could such a church be formed? The doctrine of apostolic succession might seem to be the answer: that the authority and commission of Christ had been transmitted, generation by generation, from his own time to the present. But that would mean that a wholly false church, the papal Antichrist, could in its impurity faithfully preserve and rightly pass on a wholly pure power. And that made no sense at all. After Constantine, a true ministry no longer existed, and none but God could now bring it back. Williams did not come to this position easily, nor did he find it easy to persuade others that recreating the true church of Christ was a vain pursuit -- apart from direct divine intervention. (Edwin S. Gaustad, Liberty of Conscience: Roger Williams in America, Eerdmans Publishing, Grand Rapids, MI, 1991, p. 91).
Let's use an analogy to explain what is meant by "prevail." In a football game, assume that team A gets off to a 20 to nothing lead in the first minute of the game, and team A maintains that lead until the last minute of the game. Suddenly, in the last 60 seconds, team B scores four quick touchdowns and wins the game 28 to 20. Who has "prevailed"? The team that lead for 58 minutes, or the one that was ahead at the end of the game? Obviously, it would be team B who was ahead at the end of the game. At the culmination of history, Christ's church will also reign triumphant.
Some say that there was only a "partial" apostasy suggesting that the church merely needed reforming, not restoring. But isn't that a little like being "partially" pregnant? Can there really be such a thing as a "partial" apostasy? Regarding Roger Williams, Gaustad again writes:
For Williams, who wrote of the "restless unsatisfiedness of my soul," found no enduring peace, not even in the church molded by his own hands. What authority did he have to be baptized or to baptize others? What line of apostolic continuity could be traced to that score of Bible believers who agreed to worship together? What biblical commission or divine command set this church apart or perhaps even above all others? .... In writing to John Winthrop as early as 1636, Williams bemoaned the spiritual nakedness of New England's churches but added the hope that within a few years the Lord would reveal "the first and most ancient path" more plainly "to you and me." More than a dozen years later, in a letter to Winthrop's son, Williams indicated that he found no churches organized "after the first pattern" .... As he came to appreciate the New Testament pattern more fully, Williams gradually reached a much-dreaded conclusion -- namely, that no true church of Jesus Christ was possible, at least not until Christ came again. (Edwin S. Gaustad, Liberty of Conscience: Roger Williams in America, Eerdmans Publishing, Grand Rapids, MI, 1991, p. 90-91).
More important than the terms we use to diagnose the condition of Christ's church are the solutions that the Reformation and the Restoration use to repair damage done and return to the truth of the New Testament. Some Reformers like Martin Luther wanted to remove the epistle of James from the New Testament canon and reformulate Christ's message around a "faith alone" gospel. Others like John Calvin often attempted to alter Christian thinking by sheer force of intellect rather than revelation from God.
The Restoration teaches believers to ask God and test what they receive by scripture (James 1:5 & Acts 17:10-11). The fact is that Christ's New Testament church consisted of more than simply a gathering of believers. His church was founded on the rock of the revelation of Jesus Christ, and that is the same means that he commands every believer to use to obtain truth and direction for their lives: revelation.
As Roger Williams admitted, there was no line of continuity that could be traced back to the New Testament church via Catholicism. The powers of hell will eventually face total and unquestionable defeat, but until that time, New Testament prophecy indicates that apostasy would be possible and even likely to occur.