The Great Apostasy [Mormonism labels ALL Protestant, Catholic & Orthodox churches 'apostate']

The Great Apostasy [Mormonism labels ALL Protestant, Catholic & Orthodox churches 'apostate']
Mormonism Research Ministry ^ | Aaron Shafovaloff

Posted on 10/09/2013 11:14:38 AM PDT by Colofornian

Around the world the fame of Christ spreads. Men and women lift their hands to praise the name of Jesus, worshiping him as the King of kings and Lord of lords. Full of the Holy Spirit, they lift him up as their savior, redeemer, and advocate. His gospel is preached, his word is believed, and his death and resurrection are celebrated in the Lord's Supper. Millions are baptized in the name of the Father, Son, and Holy Spirit, trusting in the person and work of Christ for forgiveness of sins, eternal life, and the transformation of their heart. Hundreds of millions of Christians gather to fellowship over the risen Christ.

Yet Mormonism pats these Christians on the heads and pities them. The "one true church", Mormonism says, is found nowhere in non-Mormon Christendom. The gift of the indwelling Holy Spirit is found nowhere outside Mormonism. The God of Mormonism recognizes no missionary work, no baptism, and no communion outside The Church of Jesus Christ of Latter-day Saints as authorized. Despite patronizing us with the uninteresting affirmation that all religion has some truth in it, Mormonism still teaches that God told Joseph Smith:

"I was answered that I must join none of them, for they were all wrong; and the Personage who addressed me said that all their creeds were an abomination in his sight; that those professors were all corrupt; that: 'they draw near to me with their lips, but their hearts are far from me, they teach for doctrines the commandments of men, having a form of godliness, but they deny the power thereof.'" (Joseph Smith—History)

Mormonism teaches that Christ's church fell into what has been described as a complete and universal apostasy. Though LDS leaders cannot agree as to when this actually happened, they do agree that it must have happened. “Nothing less than a complete apostasy from the Christian religion would warrant the establishment of the Church of Jesus Christ of Latter-Day Saints” (B.H. Roberts, History of the Church 1:XL).

Evolution of the doctrine

Charles R. Harrell writes in This Is My Doctrine:

The earliest recorded LDS teachings give little indication of a universal apostasy, especially in the way it is currently understood. At first, Mormonism shared the popular evangelical sentiment that the apostasy simply consisted of a departure from gospel teachings and practices, and not the withdrawal of priesthood authority. The Book of Mormon, for example, makes no prediction of an apostasy which involves either the priesthood or the Church being taken from the earth; nor does it mention that important ordinances pertaining to exaltation (e.g., temple ordinances) would be discontinued and need to be restored. Rather, the earliest Mormon teachings of an apostasy, like those from other contemporary restorationists, spoke only of moral corruption, a clouding or perversion of the basic teachings of Christ causing “an exceedingly great many . . . to stumble” (1 Ne. 13:29), and a denial of the power of the Holy Ghost—which includes the working of miracles (2 Ne. 28:4–15; Morm. 8:26–31).

The Book of Mormon refers to the “formation” after the time of the apostles of a “great and abominable church” (1 Ne. 13:6–9, 26–28), which early Saints understood as referring primarily to the Catholic Church. But since the Book of Mormon further defined it non-denominationally as any group opposed to “the church of the Lamb of God” (1 Ne. 14:10), Saints also came to see it as referring to any religion or government opposing God’s work. Notably, the Book of Mormon doesn’t ever suggest that the church of the Lamb would be taken from the earth, only that in the latter days, “its numbers . . . [would be] few, because of the wickedness and abominations of the whore who sat upon many waters” (1 Ne 14:12).

Prior to 1834, there is no mention of priesthood being taken from the earth—or restored for that matter (see Chapter 4). Instead, the Lord tells the Saints in December 1832, “The priesthood hath continued through the lineage of your fathers . . . therefore your life and the priesthood have remained” (D&C 86:8–10; emphasis mine). It isn’t until several years after the restoration of the Church that apostasy narratives began to include a loss of authority along with essential saving ordinances, thus paving the way for the current LDS understanding of the Great Apostasy.

Throughout the nineteenth century and well into the twentieth century, the apostasy continued to be defined primarily as a period of gospel perversion, spiritual darkness and loss of priesthood authority. Catholicism continued to be seen by many as being the principal culprit in corrupting the church.

Current LDS historians note a cultural bias underlying early Mormon characterizations of Christianity as a corrupt morass of false teachings; moreover, there is still considerable inertia which keeps these legacy teachings alive. In his historical survey of LDS literature on the apostasy, BYU history professor Eric Dursteler observes that early LDS treatises on the apostasy were “clearly” influenced by “the highly polemical, popular, confessional, historical literature of the nineteenth century and the anticlerical literature of the eighteenth-century enlightenment.” He further notes that, although the characterization of the Middle Ages as a dark and decadent era and the Renaissance as an era of spiritual awakening has been repudiated by virtually all modern historians of the past century, “Latter-day Saint treatments of the apostasy . . . have retained much of their binary vision of the Middle Ages and Renaissance.”

With modern scholarship having an increasing influence on Mormon perceptions of history, Dursteler observes that there seems to be a growing tendency among LDS writers to “move away” from depicting the apostasy as bringing on a long period of darkness followed by the dawning of the Reformation. “Instead,” he notes, “the apostasy is depicted simply as an age in which priesthood authority did not exist.” Thus, the concept of the apostasy has shifted from a loss of spiritual gifts and truths to primarily a loss of priesthood authority.

LDS characterizations of other religions as the “church of the devil” have significantly diminished. In 1990, for example, the mock representation of Protestant ministers as hirelings of Satan was removed from the LDS temple ceremony.

BYU professor Spencer Fluhman observes:

"I don't think the early Latter-day Saints discerned a doctrinal restoration in the ways that you and I do until Nauvoo. Until Joseph Smith's teaching gravitated to those topics like the nature of God. And he began saying things in distinctive enough ways that the Latter-day Saints began to discern a real addition to their understanding of God and humanity and eternity and so on. Many of the revelations in the 1830s put forward new ideas, but the Saints didn't discern a doctrinal restoration really until the late 30s and into the Nauvoo period... In some ways the cosmos was rearranged for them in Nauvoo." (BYU professor Spencer Fluhman, Mormon Identity)

True to the Faith, a currently used "correlated" booklet, summarizes the Great Apostasy this way:

"After the deaths of the Savior and His Apostles, men corrupted the principles of the gospel and made unauthorized changes in Church organization and priesthood ordinances. Because of this widespread wickedness, the Lord withdrew the authority of the priesthood from the earth. During the Great Apostasy, people were without divine direction from living prophets. Many churches were established, but they did not have priesthood power to lead people to the true knowledge of God the Father and Jesus Christ. Parts of the holy scriptures were corrupted or lost, and no one had the authority to confer the gift of the Holy Ghost or perform other priesthood ordinances. This apostasy lasted until Heavenly Father and His Beloved Son appeared to Joseph Smith in 1820 and initiated the restoration of the fulness of the gospel. We now live in a time when the gospel of Jesus Christ has been restored. But unlike the Church in times past, The Church of Jesus Christ of Latter-day Saints will not be overcome by general apostasy. The scriptures teach that the Church will never again be destroyed (see D&C 138:44; see also Daniel 2:44)"

Today, Mormonism associates the Great Apostasy with a:

loss of priesthood authority
loss of authoritative, prophetic revelation
loss of apostolic succession
loss of hierarchical, organizational unity
loss of charismatic spiritual gifts & experiences (visions, tongues, angelic visitations, healings, prophecy)
removal of Christ's name from the name of the church
changes to the ordinances
corruption of scriptures
corruption of theology
corruption of individual morality
paid clergy

Mormons see the Restoration of the LDS Church as a reversal of the above.

Soft vs. harsh definitions

Depending on the context and person either a soft or harsh definition is used for "Great Apostasy." Soft Mormon definitions of "apostasy" are minimized to the loss of priesthood authority. More harsh Mormon definitions of "apostasy" encompass the loss of any true, faithful Christians. At the very least, in this view the professing Christians grovel in spiritual darkness, being under the power of Satan himself. The common New Testament prooftexts used by Mormons for the Great Apostasy usually operate with a more harsh Mormon definition, but when scrutinized, Mormons will often revert to a minimal or soft definition. Mormons are in a tough spot today, wanting simultaneously to affirm their traditional and scriptural teachings on the Great Apostasy (replete with harsh, sweeping moral indictments), yet generalizing these "apostate" Christians as having good intentions and the light of Christ.

Examples of the "harsh" approach

"Because of these things which are taken away out of the gospel of the Lamb, an exceedingly great many do stumble, yea, insomuch that Satan hath great power over them." (1 Nephi 13:29)
“I was answered that I must join none of them, for they were all wrong; and the Personage who addressed me said that all their creeds were an abomination in his sight; that those professors were all corrupt; that: "they draw near to me with their lips, but their hearts are far from me, they teach for doctrines the commandments of men, having a form of godliness, but they deny the power thereof." (Joseph Smith—History 1:19)
“…for I contend that the Latter-day Saints are the only good and true Christians, that I know anything about in the world. There are a good many people who profess to be Christians, but they are not founded on the foundation that Jesus Christ himself has laid” (Joseph F. Smith, November 2, 1891, [Stake conference message], Collected Discourses, 2:305).
“In the days of Jesus, wicked and evil men separated themselves from the true Christians by defaming the name of Jesus and cursing him as a false prophet. In our day the same approach is made by ill-disposed persons to the name of Joseph Smith. The way men feel about him and his prophetic successors divides true believers from those who serve another master” (Bruce R. McConkie, “The Caravan Moves On,” Ensign (Conference Edition), November 1984, p.82).
"Sadly, what happened to the Lord's Church in the Mediterranean world happened to its counterpart in the Americas as well. Because of pride, those who once had been followers of Christ 'did dwindle in unbelief and wickedness' (4 Ne. 1:34) until the Church of Christ was no longer in existence. In the Old World, Christianity continued, albeit in a different form. But in the New World, every vestige of it was soon removed or thoroughly perverted to the point that the gospel was completely obliterated from the memories of later generations. We are not aware of the Church of Jesus Christ existing anywhere on earth after the close of the Book of Mormon." (Kent P. Jackson, From Apostasy to Restoration, ch. 3)
“Here is divine authority. Do any of our friends or neighbors make such a claim? We know the claim of the Catholic church, and all we say in response is that ‘By their fruits ye shall know them.’ These were the words of our Savior, and that is enough on that score. But our Protestant friends do not even have that much of a claim. They have a form of godliness, but deny the power thereof. And because they do not have the authority themselves they think no one else has” (Charles W. Nibley, Conference Reports, October 1926, p. 24).
“How, we inquire, can Christianity have been perpetuated, while its virtues, its legitimate powers, its distinguishing features, its very life and essence have ceased from among men? Or, of what use is it if it does exist? Is a compass of use when its needle has lost its magnetic attraction? Is water of use when it no longer seeks its level, or quenches thirst? Is fire of use when it loses its heat? Is a sun dial of use on a dark and cloudy day; or a watch without a mainspring? Or, are the mere forms and ceremonies of any system of use, when the divine, or legitimate powers, for which such forms were instituted, are withdrawn? O man! be no longer deceived by solemn mockeries of things sacred, or by great and holy names applied to corrupt and degenerate systems. When the miracles and gifts of the divine Spirit ceased from among men, Christianity ceased, the Christian ministry ceased, the Church of Christ ceased. That ministry which sets aside modern inspiration, revelation, prophecy, angels, visions, healings, etc., is not ordained of God, but is anti-christian in spirit. In short, it is that spirit of priestcraft and kingcraft by which the world, for many ages, has been ruled as with a rod of iron. The sooner the present generation lose all reverence and respect for modern ‘Christianity’ with all its powerless forms and solemn mockeries, the sooner they will be prepared to receive the kingdom of God. The sooner the treasuries of nations, and the purses of individuals, are relieved from the support of priestcraft and superstitions, so much sooner will they be able and willing to devote their means and influence to print and publish the glad tidings of the fullness of the Gospel, restored in this age, to assist in the gathering of the house of Israel, and in the building of the cities and temples of Zion and Jerusalem” (Parley P. Pratt, Key to the Science of Theology, 1978, pp. 67-68).
“After the ascension of Jesus, the Church remained, for some time, fully organized. Thousands flocked to it, and the members lived in accordance with the doctrine taught by the Savior. Soon, however, history repeated itself. In the right of their free agency, those who had joined the Church often refused to obey the laws and ordinances of the Gospel, and more often changed them to suit their own convenience. Such departures from the truth became more numerous and flagrant as time wore on, until error permeated the whole Church. At last, about six hundred years after Christ, the Gospel laws and ordinances had become so completely warped that it was as if the Church had departed from the earth. The authority of the Priesthood no longer remained with the Church. This was the great apostasy. From that time, universal darkness reigned upon earth for many centuries” (John A. Widtsoe, Priesthood and Church Government, p. 25).
“Let me explain, when I use the term ‘corrupt’ with reference to these ministers of the gospel, that I use it in the same sense that I believe the Lord used it when he made that declaration to Joseph Smith, the prophet, in answer to the prophet’s prayer. He did not mean, nor do I mean, that the ministers of religion are personally unvirtuous or impure. I believe as a class they, perhaps, in personal purity, stand a little above the average order of men. When I use the term ‘corrupt’ I mean, as I believe the Lord meant, that they have turned away from the truth, the purity of the truth, the beauty of the truth, and have turned to that which is false. A false doctrine is a corrupt doctrine; a false religion is a corrupt religion; a false teacher is a corrupt teacher. Any man who teaches a false doctrine, who believes in and practices and teaches a false religion is a corrupt professor, because he teaches that which is impure and not true. That is the trouble with Christianity today. It is not true. Christianity is, perhaps, no truer or falser than any other religion, than Mohammedanism, Confucianism, Buddhism or any other ism or philosophy. In fact, my brethren and sisters, if the falsity of a religion can be measured in any degree by the amount of trouble and turmoil and strife and bitterness and hatred that it has engendered in the hearts of men, if it can be judged by the number of wars it has carried on and the rivers of blood it has shed, the amount of misery and sorrow, it has caused, or the extremes of impurity, found among its adherents, then Christianity, that which is known as Christianity, is the falsest of all religions in the world. (Hyrum M. Smith, Conference Reports, October 1916, p. 43).
“After our Lord’s first coming and before his dreadful return, there is to be a day of absolute, total, and complete apostasy from the truth. Men are to be left to themselves, wanderers in darkness, without hope and without God in the world” (Bruce R. McConkie, The Millennial Messiah: The Second Coming of the Son of Man, p. 36).
“As we gaze in awe at the grand picture, we see the Lord Jesus ascending from Olivet as angelic witnesses testify that he shall come again in like manner at that place. From this splendid scene our eyes turn to the dark and dire and devilish days when Satan has dominion over his own. We see false churches, false worship, and false prophets. Iniquity abounds and evil is everywhere. There is universal apostasy; darkness covers the earth and gross darkness the minds of the people; it is the evil night that must precede the dawn of the restoration” (Bruce R. McConkie, The Millennial Messiah: The Second Coming of the Son of Man, p. 563).
“There is to be absolute, total, complete apostasy after John’s day and before the angelic ministrations commence. The falling away shall be complete, the apostasy universal. Gross darkness shall be everywhere. The gospel shall not be found in any nation, among any kindred; no tongue shall teach its truths, and no people rejoice in its blessings, for all these shall receive it as a result of the angelic ministrations” (Bruce R. McConkie, Doctrinal New Testament Commentary 3:528).
“If the Savior had come back to earth at the beginning of the fifth century A.D., I doubt whether he would have recognized the Christian Church as the one that claimed descent from that which he had established, so far had it gone astray. Christianity had actually become a composite of Christian beliefs, practices, and doctrines, Jewish teachings and rituals; Greek, Roman, and Egyptian pagan philosophies: and pagan religions of various brands. The Holy Priesthood had been withdrawn from the earth. The power of godliness was no longer present in the Christian Church. Thus there was a complete falling away from the gospel which had been established by the Son of Man. The Church lay in darkness, and the darkness enveloped the earth. This spiritual darkness continued for hundreds and hundreds of years” (Milton R. Hunter, Conference Reports, October 1951, pp. 140-141).
“What can we say of the original Church in the light of history, after it had existed one hundred years? There was very little left of it. The apostasy which commenced to show itself in the days of Paul had spread to such an extent that after the great lights of the Church had fallen as martyrs, the great majority of the Saints had turned away from the gospel as originally taught by the Savior” (Andrew Jensen, Conference Reports, April 1924, pp. 136-137).
“Thus a mist of darkness filled the earth in what we have come to call a universal apostasy. It engulfed the priesthood, its keys, all the ordinances of salvation and the ordinances of blessing, and the offices of the priesthood and its officers. Plain and precious things were taken from holy writ, and other things were added in their place. The purity of every doctrine and principle of salvation was lost. In their stead came an oppressive tyranny over the hearts and minds of men. Where once there had been love unfeigned, now there was a blood-stained sword. Where there had been robes of righteousness, now there were silks, and scarlets, and fine-twined linen, and precious clothing. Worship was replaced by ritual; the prayer of faith, by gold and silver. So darkness covered the earth and gross darkness the minds of the people (see Isaiah 60:2)” (BYU Professor Emeritus Joseph Fielding McConkie, Answers: Straightforward Answers to Tough Gospel Questions, p. 39)
“But who in this generation have authority to baptize? None but those who have received authority in the church of Jesus Christ of Latter day Saints: all other churches are entirely destitute of all authority from God; and any person who receives Baptism or the Lord’s supper from their hands will highly offend God, for he looks upon them as the most corrupt of all people. Both Catholics and Protestants are nothing less than the 'whore of Babylon' whom the Lord denounces by the mouth of John the Revelator as having corrupted all the earth by their fornications and wickedness. And any person who shall be so wicked as to receive a holy ordinance of the gospel from the ministers of any of these apostate churches will be sent down to hell with them, unless they repent of the unholy and impious act.”(Apostle Orson Pratt, The Seer, p. 255)

Example of the "soft" approach

“Our position is this: While there was this universal apostasy, while the Church of Christ as an organization was destroyed, and replaced by the churches of men, yet just as when the sun goes down, there still remains light in the sky-so, too, notwithstanding this apostasy from the Church, there still were left fragments of truth among the children of men, and some measure of truth thank God, through his mercy, has always remained with man, not only with Christians but with all God’s children. He has not left himself in any of the ages of the world without his witnesses, and he has sanctified all generations of men with some measure of the truth; therefore, when we proclaim this apostasy from the Christian religion and the destruction of the Church of Christ, it does not follow that we hold that all truth, that all virtue, had departed from the world, or that God had absolutely withdrawn from his creation. Not so” (B.H. Roberts, 1992, Defense of The Faith and The Saints 2:561).
"We see ourselves as a part of the larger Christian world, and we have no difficulty acknowledging that our Christian friends worship the same God we do, seek the redeeming power of the same Savior we do, and enjoy the illuminating and sanctifying influence of the same Holy Spirit we do. Now, to be sure, Latter-day Saints do believe they have something to add to the great reservoir of Christian truth in the world—important theological insights, as well as a broadened perspective on the purpose of life and the eternal destiny of individuals and families." (Robert Millet, "Traditional Christianity and the Latter-day Saints", LDS Newsroom)
“Let me say that we appreciate the truth in all churches and the good which they do. We say to the people, in effect, you bring with you all the good that you have, and then let us see if we can add to it. That is the spirit of this work. That is the essence of our missionary service.” (Gordon B. Hinckley, “Excerpts from Recent Addresses of President Gordon B. Hinckley,” Ensign, Aug 1998, 72)

The gospel itself, lost from the earth?

"As members of The Church of Jesus Christ of Latter-day Saints the Lord has admonished us to be ‘ready always to give an answer to every man, for our faith in the restored gospel.’ This we owe to the inhabitants of this mortal world. For hundreds of years, following the universal apostasy, the inhabitants of the earth walked in spiritual darkness. They became divided and sub-divided. Satan had obtained such power over their thinking that the fundamental principles of the gospel ceased to exist among them” (Joseph Fielding Smith, Answers to Gospel Questions 5:xi).
“This is not a continuous church, nor is it one that has been reformed or redeemed. It has been restored after it was lost. It was lost – the gospel with its powers and blessings – Sometime after the Savior’s crucifixion and the loss of his apostles. The laws were changed, the ordinances were changed, and the everlasting covenant was broken that the Lord Jesus Christ gave to his people in those days. There was a long period of centuries when the gospel was not available to people on this earth, because it had been changed” (The Teachings of Spencer W. Kimball, p. 423).
“There is to be absolute, total, complete apostasy after John’s day and before the angelic ministrations commence. The falling away shall be complete, the apostasy universal. Gross darkness shall be everywhere. The gospel shall not be found in any nation, among any kindred; no tongue shall teach its truths, and no people rejoice in its blessings, for all these shall receive it as a result of the angelic ministrations” (Bruce R. McConkie, Doctrinal New Testament Commentary 3:528).

Mormon Prooftexts

Old Testament

Amos 8:11
Passage: "Behold, the days come, saith the Lord God, that I will send a famine in the land, not a famine of bread, nor a thirst for water, but of hearing the words of the Lord."
Explanation: "Biblical scholars explain that, in its historical context, the 'famine' alluded to in this passage refers to the imminent consequence of the wickedness and apostasy of ancient Israel as seen in the Assyrian conquest (see Amos 7:11).7 Similar mention of this state of spiritual depravity in ancient Israel can be found in other writings in the wake of the Babylonian captivity (e.g., Isa. 29:10). Amos is telling the Israelites that, although at present they have prophets to tell them the word of the Lord, 'the days [will] come' (in their captivity) when they will no longer have access to God’s words. This prophecy was uttered around 760 B.C. and Israel was invaded by the Assyrians about 40 years later. Echoing the view of other Old Testament scholars, BYU religion professor D. Kelley Ogden comments, 'Amos’s mission was to warn Israel of its present disastrous state and forewarn it of impending captivity.' He further notes that 'Amos’s prophecies [including this one] were fulfilled, soon by the Assyrians and then later by other conquerors.' While the language of these Old Testament prophecies may contain apt descriptions of the spiritual depravity of our modern day—and for that matter almost any other period of history—the scholarly consensus is that in their original context, these prophecies were expressly directed at ancient Israel’s apostate condition." (Harell, ch. 2)
Isaiah 24:5
Passage: "The earth also is defiled under the inhabitants thereof; because they have transgressed the laws, changed the ordinance, broken the everlasting covenant."
Explanation: "According to biblical scholars, the 'everlasting covenant' in Isaiah 24 has reference to the law of Moses, which ancient Israelites understood would stand 'forever' as an 'everlasting' or 'perpetual covenant' and would remain in effect 'throughout generations' (Ex. 12:14, 17, 24; Lev. 3:17; 16:34; 17:7). The Israelites were guilty of violating this law, particularly its regulations prohibiting murder (see Ex. 20:13; Num. 35:31–34; Gen. 9:1–7). According to Mosaic law, murder defiles the land and brings upon it the curse of God. The Israelites’ shedding of innocent blood had defiled the land (see Isa. 1:15, 21; 4:4), 'therefore, hath the curse [spelled out in the law] devoured the earth' (Isa. 24:6). In short, Isaiah 24:5 is seen by most Old Testament scholars as a direct commentary on Israel’s flagrant violation of the law of Moses in Isaiah’s day, though certainly the language may have been well suited to describe the perceived situation in Joseph Smith’s day." (Harrell, ch. 2)
Isaiah 29:13-14
Passage: "Wherefore the Lord said, Forasmuch as this people draw near me with their mouth, and with their lips do honour me, but have removed their heart far from me, and their fear toward me is taught by the precept of men: Therefore, behold, I will proceed to do a marvellous work among this people, even a marvellous work and a wonder: for the wisdom of their wise men shall perish, and the understanding of their prudent men shall be hid."
Explanation: "Joseph Fielding Smith commented, 'This marvelous work is the restoration of the Church and the Gospel with all the power and authority, keys and blessings which pertain to this great work for the salvation of the children of men.' Prior to the organization of the Church in 1830, Isaiah’s 'marvelous work and a wonder' was understood by Mormons in a slightly different light than it is today. In the Book of Mormon, for instance, the 'marvelous work and a wonder' wasn’t the restoration of the Church and gospel, but the temporal and spiritual gatherings of Israel in the last days, mainly through the instrumentality of the Book of Mormon (1 Ne. 14:7; 2 Ne. 25:17–18; 29:1, 7). Similarly, early revelations in the Doctrine and Covenants exclusively reference the 'marvelous work and a wonder' as the gathering of the righteous as they hear and accept the gospel contained in the Book of Mormon (D&C 4:1; 6:1; 11:1; 12:1; 14:1; 18:44). Once the translation of the Book of Mormon was completed, almost a year before the Church was founded, scriptural references to a 'marvelous work and a wonder' ceased. When read in context, the 'marvelous work and a wonder' (NRSV = 'things . . . shocking and amazing') in Isaiah appears to refer to God’s work of vengeance on the ungodly, not his blessing of the righteous. The Lord declares, 'Forasmuch as this people . . . have removed their heart far from me . . . I will proceed to do a marvellous work among this people, even a marvellous work and a wonder for the wisdom of their wise men shall perish, and the understanding of their prudent men shall be hid' (Isa. 29:13–14). It will be a wonder 'for' (i.e., because) the wisdom of the wise shall perish. God’s wonderful and marvelous works are not always positive in nature (see, for example, the 'wonderful' plagues described in Deut. 28:59).45 This may explain why the very next verse reads, 'Woe unto them that seek deep to hide their counsel from the Lord' (Isa. 29:15).'" (Harrell, ch. 4)
Isaiah 60:2
Passage: "For, behold, the darkness shall cover the earth, and gross darkness the people: but the Lord shall arise upon thee, and his glory shall be seen upon thee."

New Testament

As a rule of thumb, texts Mormons use to support the Great Apostasy from the New Testament usually either:

are in a context where the author is encouraging and ensuring readers to endure through the dark time spoken of.
culminate in the Second Coming, not in the restoration of the church.
don't fulfill the needed conditions for a universal "great apostasy" where the Christian church literally ceases to exist; rather, speak of a moral failing or apostasy of individuals that ought be remedied with spiritual renewal and refocus on the scriptures (i.e. reformation).

Harell writes:

"On careful examination, none of the New Testament passages referring to heresies within the church or persecution from without seems to predict a wholesale departure from the faith; all seem to assume that there would be faithful saints who remain on the earth until Christ comes. Miami University New Testament professor Roy Ward observed that every prediction of an apostasy in the New Testament and other apocalyptic literature 'always assumes that the righteous will have a continuing existence until the end, despite the apostasia.'" (ch. 2)

Matthew 24:24
Passage: "For there shall arise false Christs, and false prophets, and shall shew great signs and wonders; insomuch that, if it were possible, they shall deceive the very elect."
Acts 3:19-21
Passage: "Repent ye therefore, and be converted, that your sins may be blotted out, when the times of refreshing shall come from the presence of the Lord; And he shall send Jesus Christ, which before was preached unto you: Whom the heaven must receive until the times of restitution of all things, which God hath spoken by the mouth of all his holy prophets since the world began."
Explanation: "Considering the context of Peter's remarks and the eschatological expectations of his audience, the passage is most naturally interpreted as referring to the final establishment of the Messianic kingdom, when Christ shall reign over a world purified of sin." (source)
Acts 20:29-30
Passage: "For I know this, that after my departing shall grievous wolves enter in among you, not sparing the flock. Also of your own selves shall men arise, speaking perverse things, to draw away disciples after them."
2 Thessalonians 2:2-3
Passage: "That ye be not soon shaken in mind, or be troubled, neither by spirit, nor by word, nor by letter as from us, as that the day of Christ is at hand. Let no man deceive you by any means: for that day shall not come, except there come a falling away first, and that man of sin be revealed, the son of perdition."
1 Timothy 4:1-3
Passage: "Now the Spirit speaketh expressly, that in the latter times some shall depart from the faith, giving heed to seducing spirits, and doctrines of devils; Speaking lies in hypocrisy; having their conscience seared with a hot iron; Forbidding to marry, and commanding to abstain from meats, which God hath created to be received with thanksgiving of them which believe and know the truth."
2 Timothy 3:1-7
Passage: "This know also, that in the last days perilous times shall come. For men shall be lovers of their own selves, covetous, boasters, proud, blasphemers, disobedient to parents, unthankful, unholy, without natural affection, trucebreakers, false accusers, incontinent, fierce, despisers of those that are good, traitors, heady, highminded, lovers of pleasures more than lovers of God; Having a form of godliness, but denying the power thereof: from such turn away. For of this sort are they which creep into houses, and lead captive silly women laden with sins, led away with divers lusts, ever learning, and never able to come to the knowledge of the truth."
2 Timothy 4:3-4
Passage: "For the time will come when they will not endure sound doctrine; but after their own lusts shall they heap to themselves teachers, having itching ears; and they shall turn away their ears from the truth, and shall be turned unto fables."
2 Peter 2:1-2
Passage: "But there were false prophets also among the people, even as there shall be false teachers among you, who privily shall bring in damnable heresies, even denying the Lord that bought them, and bring upon themselves swift destruction. And many shall follow their pernicious ways; by reason of whom the way of truth shall be evil spoken of."
Jude 4
Passage: "For there are certain men crept in unawares, who were before of old ordained to this condemnation, ungodly men, turning the grace of our God into lasciviousness, and denying the only Lord God, and our Lord Jesus Christ."
Revelation 12:6
Passage: "And the woman fled into the wilderness, where she hath a place prepared of God, that they should feed her there a thousand two hundred and threescore days."
Revelation 14:6
Passage: "And I saw another angel fly in the midst of heaven, having the everlasting gospel to preach unto them that dwell on the earth, and to every nation, and kindred, and tongue, and people."
Explanation: "The burden of the angel's message, which sets the theme for the remainder of the chapter, is not one of salvation or restoration but of impending doom. It is a particular aspect of the everlasting gospel that is proclaimed by the angel, one composed of fearful judgment rather than Christian hope. The angel, furthermore, is not represented as visiting the earth but as proclaiming his message in mid-heaven; his message is not heard by a select few but by all the inhabitants of the earth." (source)

Passages that refute the Great Apostasy

Did a Universal Apostasy and Restoration Really...

Matthew 16:18
Passage: "And I tell you, you are Peter, and on this rock I will build my church, and the gates of hell shall not prevail against it."
Explanation: "With New Testament saints anxiously anticipating Jesus’s imminent return, it seems unlikely that they would have anticipated the church falling into a complete state of apostasy. Indeed, there are several indications that they believed the church was here to stay. Consider Christ’s words to Peter: 'Thou art Peter, and upon this rock I will build my church; and the gates of hell shall not prevail against it' (Matt. 16:18). Many scholars view the pronoun 'it' as having reference to the apostolic church, others to the invisible church or body of believers, and still others to revelation or the inspired witness of Christ on which the church is built.13 Often the interpretation given is influenced by one’s religious tradition: Catholic, Protestant or Mormon. In the traditional Mormon interpretation, 'the gates of hell should never prevail against the rock of revelation.'14 Whatever the interpretation, most commentators agree that there was some essential aspect of the church that was to persevere or endure. In Christ’s last commission to his disciples to preach the gospel to all nations, he reassured them saying, 'Lo, I am with you alway, even unto the end of the world' (Matt. 28:20), or as rendered in several modern translations, 'to the end of time.' Warnings of apostasy, therefore, need to be weighed against assurances of perseverence and continuity. New Testament scholar Paul Barnett explains, 'While many warnings are given of the dangers of falling away, there are also encouragements about the mercy of God shown in these situations (e.g. Heb. 4:14–16) as well as the strength and faithfulness of God to ‘keep’ his children from falling away from the true path of faith (e.g., 1 Pet. 1:5; 2 Pet. 2:9; 1 John 4:4; Jude 1:24; Rev. 3:10).'" (Harrell, ch. 2)
Contrast:
+ "Jesus made his appearance on the earth in the meridian of time, and he established his kingdom on the earth. But to fulfill ancient prophecies the Lord suffered that kingdom to be uprooted; in other words, the kingdoms of this world made war against the kingdom of God, established eighteen centuries ago, and they prevailed against it, and the kingdom ceased to exist. The great beast that John saw made war with it and prevailed against it, and human institutions, without prophets or inspired men, usurped the place of the ancient kingdom of God. But God has promised that the latter-day kingdom shall stand forever." (Orson Pratt, Journal of Discourses 13:125)
+ "Satan was given power to overcome the saints in former days, and the persecutions he waged against them and the officers of the Church contributed to his passing success. It has been decreed that he shall not have power to destroy the Church in the last dispensation [started in the 19th century], and his persecution of the saints today will be futile as a means of bringing about a general apostasy in these latter times." (James Talmage, The Great Apostasy Considered in the Light of Scriptural and Secular History, p. 61)
Matthew 28:18-20
Passage: "All authority in heaven and on earth has been given to me. Go therefore and make disciples of all nations, baptizing them in the name of the Father and of the Son and of the Holy Spirit, teaching them to observe all that I have commanded you. And behold, I am with you always, to the end of the age."
Ephesians 3:21
Passage: "To him be glory in the church and in Christ Jesus throughout all generations, forever and ever. Amen."
Hebrews 12:28-29 (cf. Daniel 2:44)
"Therefore let us be grateful for receiving a kingdom that cannot be shaken, and thus let us offer to God acceptable worship, with reverence and awe, for our God is a consuming fire."
Romans 11:2-6
Passage: "God has not rejected his people whom he foreknew. Do you not know what the Scripture says of Elijah, how he appeals to God against Israel? 'Lord, they have killed your prophets, they have demolished your altars, and I alone am left, and they seek my life.' But what is God's reply to him? 'I have kept for myself seven thousand men who have not bowed the knee to Baal.' So too at the present time there is a remnant, chosen by grace."
Jude 1:24
Passage: "Now to him who is able to keep you from stumbling and to present you blameless before the presence of his glory with great joy..."
Acts 2:47
"And the Lord added to their number day by day those who were being saved."
Parable of the Leaven (Matthew 13:33; Luke 13:20–21)
Passage: "The kingdom of heaven is like leaven that a woman took and hid in three measures of flour, till it was all leavened." (Matthew 13:33)
Contrast: "This seems to convey the same idea as the other parables—a gradual, spreading growth of the kingdom Christ established. According to Joseph Smith, however, this parable refers to the latter days as 'the Church of the Latter-day Saints, has taken its rise from a little leaven that was put into three witnesses.' [Joseph Smith, 'To the Elders of the Church of the Latter Day Saints,' 228] Later still, he saw other meanings in the three measures of meal, including, in December 1842, 'the three in the Grand Presidency.' [History of the Church, 5:207]" (Harrell, ch. 2)
Parable of the Mustard Seed (Matthew 13:31-32, Mark 4:30-32, and Luke 13:18-19)
Passage: "The kingdom of heaven is like a grain of mustard seed that a man took and sowed in his field. It is the smallest of all seeds, but when it has grown it is larger than all the garden plants and becomes a tree, so that the birds of the air come and make nests in its branches." (Matthew 13:31-32)
Contrast: "The parable of the mustard seed... indicates that the kingdom Christ set up was to begin small but would gradually grow into a large, mature tree. Joseph Smith, however, interpreted the parable as representing 'the Church as it shall come forth in the last days,' with the mustard seed symbolizing the Book of Mormon sprouting out of the earth. [Joseph Smith, “To the Elders of the Church of the Day Saints,” 227]" (Harrell, ch. 2)
Parable of the Wheat and Tares (Matthew 13:24-30; 36-43)
Passage: "He put another parable before them, saying, “The kingdom of heaven may be compared to a man who sowed good seed in his field, but while his men were sleeping, his enemy came and sowed weeds among the wheat and went away. So when the plants came up and bore grain, then the weeds appeared also. And the servants of the master of the house came and said to him, ‘Master, did you not sow good seed in your field? How then does it have weeds? He said to them, ‘An enemy has done this.’ So the servants said to him, ‘Then do you want us to go and gather them?’ But he said, ‘No, lest in gathering the weeds you root up the wheat along with them. Let both grow together until the harvest, and at harvest time I will tell the reapers, Gather the weeds first and bind them in bundles to be burned, but gather the wheat into my barn.’” ... Then he left the crowds and went into the house. And his disciples came to him, saying, “Explain to us the parable of the weeds of the field.” He answered, “The one who sows the good seed is the Son of Man. The field is the world, and the good seed is the sons of the kingdom. The weeds are the sons of the evil one, and the enemy who sowed them is the devil. The harvest is the end of the age, and the reapers are angels. Just as the weeds are gathered and burned with fire, so will it be at the end of the age. The Son of Man will send his angels, and they will gather out of his kingdom all causes of sin and all law-breakers, and throw them into the fiery furnace. In that place there will be weeping and gnashing of teeth. Then the righteous will shine like the sun in the kingdom of their Father. He who has ears, let him hear."
Explanation: "This altered rendering changes the sense of the parable from the biblical account—preserved also in JST Matthew (revised in the spring of 1832)—where the wheat wasn’t choked, but continued to grow and was gathered safely into the barn. There is never any mention, even in the New Testament interpretation of the parable (Matt. 13:37–43), that 'the children of the kingdom' would be overcome or that a second growing season (i.e., restoration) would be necessary. The parable as it stands consistently fits the New Testament perspective that the kingdom would survive any perils until the Savior’s return." (Harrell, ch. 2)
Contrast:
+ "And after they have fallen asleep the great persecutor of the church, the apostate, the whore, even Babylon, that maketh all nations to drink of her cup, in whose hearts the enemy, even Satan, sitteth to reign—behold he soweth the tares; wherefore, the tares choke the wheat and drive the church into the wilderness. But behold, in the last days, even now while the Lord is beginning to bring forth the word, and the blade is springing up and is yet tender." (D&C 86:3-4)
+ "Interestingly, Joseph Smith reverted to this more natural reading of the parable in December 1835, stating that the Savior was essentially telling his disciples, 'The Church is in its infancy, and if you take this rash step [i.e., remove the tares], you will destroy the wheat or the Church with the tares: therefore it is better to let them grow together until the harvest, or the end of the world.' [Joseph Smith, 'To the Elders of the Church of the Latter Day Saints,' 227.]" (Harrell, ch. 2)
+ “In like manner the saints in the early days of the Christian era soon forsook the faith. Tares were sown in the gospel fields. And ‘the apostate, the whore, even Babylon, that maketh all nations to drink of her cup, in whose hearts the enemy, even Satan, sitteth to reign’ — even he took over the kingdom. (D&C 86:3.) The apostasy was complete and universal” (Bruce R. McConkie, The Millennial Messiah: The Second Coming of the Son of Man, p. 425).

Jesus as the groom, friend, shepherd, and true vine

Groom (Ephesians 5:22-33)
Passage: "Wives, submit to your own husbands, as to the Lord. For the husband is the head of the wife even as Christ is the head of the church, his body, and is himself its Savior. Now as the church submits to Christ, so also wives should submit in everything to their husbands. Husbands, love your wives, as Christ loved the church and gave himself up for her, that he might sanctify her, having cleansed her by the washing of water with the word, so that he might present the church to himself in splendor, without spot or wrinkle or any such thing, that she might be holy and without blemish. In the same way husbands should love their wives as their own bodies. He who loves his wife loves himself. For no one ever hated his own flesh, but nourishes and cherishes it, just as Christ does the church, because we are members of his body. 'Therefore a man shall leave his father and mother and hold fast to his wife, and the two shall become one flesh.' This mystery is profound, and I am saying that it refers to Christ and the church. However, let each one of you love his wife as himself, and let the wife see that she respects her husband."
Explanation: Why would Jesus let his bride die in her infancy? Jesus loves his bride, the church. Jesus is the head of his church, his body, his wife. He loves her, he gave himself up for her "that he might sanctify her, having cleansed her by the washing of water with the word." The church is like a man's own flesh: Jesus nourishes and cherishes the church.
Contrast: "Come on! ye prosecutors! ye false swearers! All hell, boil over! Ye burning mountains, roll down your lava! for I will come out on the top at last. I have more to boast of than ever any man had. I am the only man that has ever been able to keep a whole church together since the days of Adam. A large majority of the whole have stood by me. Neither Paul, John, Peter, nor Jesus ever did it. I boast that no man ever did such a work as I. The followers of Jesus ran away from Him; but the Latter-day Saints never ran away from me yet. You know my daily walk and conversation. I am in the bosom of a virtuous and good people. How I do love to hear the wolves howl!" (Joseph Smith, "Address of the Prophet—His Testimony Against the Dissenters at Nauvoo", History of the Church Vol. 6, p. 408-412)
Good Shepherd (John 10:7-16)
Passage: "Truly, truly, I say to you, I am the door of the sheep. All who came before me are thieves and robbers, but the sheep did not listen to them. I am the door. If anyone enters by me, he will be saved and will go in and out and find pasture. The thief comes only to steal and kill and destroy. I came that they may have life and have it abundantly. I am the good shepherd. The good shepherd lays down his life for the sheep. He who is a hired hand and not a shepherd, who does not own the sheep, sees the wolf coming and leaves the sheep and flees, and the wolf snatches them and scatters them. He flees because he is a hired hand and cares nothing for the sheep. I am the good shepherd. I know my own and my own know me, just as the Father knows me and I know the Father; and I lay down my life for the sheep. And I have other sheep that are not of this fold. I must bring them also, and they will listen to my voice. So there will be one flock, one shepherd."
"I will not leave you as orphans" (John 14:18,26)
Passage: "I will not leave you as orphans; I will come to you... The Helper, the Holy Spirit, whom the Father will send in my name, he will teach you all things and bring to your remembrance all that I have said to you."
True Vine (John 15:1-11)
Passage: "I am the true vine, and my Father is the vinedresser. Every branch in me that does not bear fruit he takes away, and every branch that does bear fruit he prunes, that it may bear more fruit. 3 Already you are clean because of the word that I have spoken to you. Abide in me, and I in you. As the branch cannot bear fruit by itself, unless it abides in the vine, neither can you, unless you abide in me. I am the vine; you are the branches. Whoever abides in me and I in him, he it is that bears much fruit, for apart from me you can do nothing. If anyone does not abide in me he is thrown away like a branch and withers; and the branches are gathered, thrown into the fire, and burned. If you abide in me, and my words abide in you, ask whatever you wish, and it will be done for you. By this my Father is glorified, that you bear much fruit and so prove to be my disciples. As the Father has loved me, so have I loved you. Abide in my love. If you keep my commandments, you will abide in my love, just as I have kept my Father's commandments and abide in his love. These things I have spoken to you, that my joy may be in you, and that your joy may be full."
Contrast: "And my vineyard has become corrupted every whit..." (D&C 33:4)
Friend (John 15:15-16)
Passage: "No longer do I call you servants, for the servant does not know what his master is doing; but I have called you friends, for all that I have heard from my Father I have made known to you. You did not choose me, but I chose you and appointed you that you should go and bear fruit and that your fruit should abide, so that whatever you ask the Father in my name, he may give it to you."

Hypocritical standards

Prioritizing intellectuals over apostles and prophets as cause for apostasy

BYU professor Kent P. Jackson writes:

"Though pagans and persecutors often caused difficulties for early Christians, from the historical record there is no reason to believe that persecution had anything to do with the Apostasy, and the evidence does not point to Church members abandoning the faith to revert to their ancestral paganism. Nor do the sources suggest that the Apostasy was the result of Christians becoming less active in their faith or losing interest in it. Instead, we see zealous Church members who were not content with 'sound doctrine' but still had 'itching ears' for religion (2 Tim. 4:3-4). And they did what their counterparts do in our own day. They sought out what a modern apostle has called 'alternate voices,' 5 teachers whose words they found to be more 'pleasing unto the carnal mind' (Alma 30:53)—more intellectually stimulating, more in style with contemporary ideas, or more spiritually titillating—than were the teachings of the Lord's authorized servants. In due time this process resulted in a spiritual transformation in the Church. The divinely revealed authority of apostles was replaced by the self-appointed authority of intellectuals." (From Apostasy to Restoration, ch. 3)

Yet this is precisely what is happening in modern Mormonism. Informed Mormons are prioritizing the voices of Robert Millet, Stephen Robinson, Michael Ash, Blake Ostler, Daniel Peterson, etc., over apostles and prophets like Spencer Kimball, Dallin Oaks, Richard G. Scott, Boyd K. Packer, etc. Jackson might as well be talking about Sunstone, FAIR, FARMS, or the BYU religion department.

Disregarding truth to promote the interests of the church as evidence of apostasy

Mormon apostle James Talmage writes:

"Disregard for truth. As early as the fourth century, certain pernicious doctrines embodying a disregard for truth gained currency in the Church. Thus, it was taught "that it was an act of virtue to deceive and lie, when by that means the interests of the church might be promoted." Needless to say, sins other than those of falsehood and deceit were justified when committed in the supposed interests of church advancement, and crime was condoned under the specious excuse that the end justifies the means. Many of the fables and fictitious stories relating to the lives of Christ and the apostles, as also the spurious accounts of supernatural visitations and wonderful miracles, in which the literature of the early centuries abound, are traceable to this infamous doctrine that lies are acceptable unto God if perpetrated in a cause that man calls good." - The Great Apostasy, ch. 7

Other Quotes

"To say that doctrines taught in the LDS Church today are restored doctrines implies that they were previously taught in biblical times before being lost. Few of the doctrines unique to Mormonism, however, are sufficiently elucidated in the Bible to be clearly recognizable." (Charles Harrell, This Is My Doctrine)
"Our Savior organized his Church when he was in his ministry, but this was not, as generally believed, the beginning of his Church on the earth. The first church organization was given to Adam. It was in existence in the days of Enoch, Noah, Abraham and Moses. What is the Church? It is a divinely organized government, with officers and unchangeable laws, whose King is Jesus Christ. Its purpose is to bring to pass the salvation and exaltation of its citizens, through their obedience to its divine laws. A church which does not conform to the pattern, which is not in strict obedience to these laws, cannot under any other name or pretext, be the Church of Jesus Christ. Neither can any man or set of men, no matter how well organized, without divine appointment, organize the Church of Jesus Christ. All churches "ordained of men" will come to an end. Men cannot invest themselves with power to do the Lord's will." - President Joseph Fielding Smith
“Christianity did not begin with the earthly birth of Jesus. The religion that Adam and Eve were taught by God was Christianity. Then does that mean that every Old Testament prophet was a Christian? Yes, that is what we believe. From the beginning, Adam and Eve taught their children Christianity – that the Son of God would one day come to the earth, teach His doctrines in person, and then atone for (that is, make forgivable) all the sins of mankind from the beginning to the end. In time, the descendants of Adam rejected it, causing a falling away from true teachings, what we call an apostasy. Thus began a pattern: True Christianity was given to a prophet – Adam, Noah, Abraham, Moses, Isaiah, among others – followed by a falling away from those teachings.” (Gary C. Lawrence, Mormons Believe . . . What?!: Fact and Fiction About a Rising Religion, 2011)
ecclesia semper reformans, semper reformanda - "the church is always reformed and always reforming."