The result was loss all around. For each needed the other. The message that Christ is our righteousness was divinely ordained; but Waggoner's insistence that the law in Galatians 3 was only the moral law, when Paul’s argument was that circumcision and the ritual law were not a condition of salvation, reduced the confidence level, creating grist for his opponents mill. Had he acknowledged this fact it would have strengthened his message, giving force to the underlying principle that no one is justified by any law, not even the moral law. Meanwhile, intense opposition by leaders who refused to objectively examine their position caused Waggoner and Jones to see any difference from them as opposition to God and truth.

For years, Ellen White stood by their side, often testifying to the divine source of their message. But she not only reproved Jones for his arrogance at Minneapolis in his debate with Smith over the horns of Daniel, she frequently reproved his attitude and severe manner and protested a number of his extreme positions and/or expressions. She reproved him in 1890 for claiming there are no conditions to receiving Christ’s righteousness and again on April 9, 1893 for insisting “that works amounted to nothing and that there were no conditions.”

In 1894 Jones was reproved for proclaiming Anna Phillips a true prophetess. On January 14, 1894, Ellen White had reproved him, along with Waggoner, for promoting concepts that threatened church organization. She remonstrated:

“Elder Waggoner ... has agitated strange theories, he has brought before some of the people, ideas in regard to organization that ought never to have had expression. I supposed the question of organization was settled forever with those who believed the testimonies. ...

“...Oh how Satan would rejoice to get in among this people, and disorganize the work at a time when thorough organization is essential, and will be the greatest power to keep out spurious uprisings. ... Let not you nor Elder Waggoner be incautious now, and advance things that are not proper, and not in accordance with the very message God has given.”

Thus, little more than five years after Minneapolis, Jones and Waggoner threaten the very message Ellen White reminds had identified as “laying the glory of man in the dust,” which called for daily death to the self, that alone perpetuates division between committed brethren. By directing attention away from self, that message was intended to lead to unity. Yet unity requires not only humility but organization -- not individualism and independence, based on a false, anarchy stimulating concept of the role of the Holy Spirit.

This problem was no doubt still in her mind when on June 1, 1894 Ellen White wrote S. N. Haskell: “The Lord’s work needed every jot and tittle of experience that he had given Eld. Butler and Eld. Smith,” whom she blamed for not respecting the younger men. Yet, in reproving Jones, six days later she, she told him “he needed to appreciate and respect the older ‘warriors’ who were also God’s channel of truth” (see George, Knight’s (From 1888 to Apostasy, p. 74).

The proclaimers were to have been trained, with others, by humbly internalizing their own message, which from the first they undermined by their independence. Because they did then humbly respond to reproof, God blessed their efforts. But now they again threatened their message by promoting an independence that breeds self-centeredness and pride. By identifying organization with Babylon and the Papacy, they echoed the very arguments used in the 1850s to oppose James and Ellen White in their efforts to organize and unify the movement. Waggoner and Jones would not have developed the extreme ideas that caused their loss to the church had both pairs humbled themselves and sought unity in the Spirit.

Jones’ interest in organization was evident prior to 1888. For he was there slated to speak on three subjects: righteousness by faith, religious liberty, and church organization. The latter was pushed aside by discussions of righteousness by faith; but only months later (May, 1889) he presented all three at the Ottowa, Kansas camp meeting, where he proclaimed that Christ was not only the head of the church, but the head of each member of the church. Thus seeing no need for human organization, he later repudiated any organization as Papal.

Meanwhile, Waggoner, and Prescott joined Jones in preaching his three-fold message. The vital truth in their vertical priesthood of believers principle of individual responsibility to God could hardly be over-emphasized. But failure to unite this with the horizontal principle of mutual accountability created a serious imbalance. Unfortunately, the sustained opposition of key leaders who grossly violated the horizontal principle spurred on the individualism and independence that threatened the very organization which had cost James and Ellen so much effort and anguish. Thus her January 14, 1894 reproof should have come as no surprise.

Jones and Waggoner could not see that to oppose leadership and organization was to challenge Christ Himself, Whom they proclaimed. For He not only appointed and trained the twelve, but directed in replacing Judas, the lost leader. Nor did they honor Paul’s admonition, in presenting the unifying gifts of the Spirit, “him that ruleth, [do it] with diligence” (Rom 12:8), or his stronger injunction: “Remember them which have rule over you, who have spoken unto you the Word of God” Heb 13:7).

God has never left his people unorganized or without leaders. Indeed, wherever he went, Paul appointed and trained elders and deacons to bear responsibility for feeding, guiding, and protecting the flock. From Genesis to Revelation we are reminded that God is a God of thorough organization.

In 1897 Jones read an 1896 testimony, “It is not wise to choose one man as president of the General Conference” to argue for more than one General Conference. But he shortly took the extreme position that she apposed the office of president, itself. Despite his own previous interpretation, he now even claimed that it could be interpreted in no other way. Yet, that very paragraph explains why there should not be only one president: the work was too complicated and wide-spread for one to handle. Indeed, that very paragraph ends by honoring the office: “The president of the General Conference should have the privilege of deciding who shall stand by his side as counselors.” (The early Elmshaven Years, Arthur White, p. 257).

His “no presidents” theme would become a no organization insistence; Jones even denied the right of any church to discipline its members. At the 1899 General Conference Waggoner and Prescott joined, not only to oppose the office of president, but to proclaim that true organization requires individual independence. Waggoner made the extreme statement: “Perfect unity means absolute independence.” Rather than the inter-dependence called for in true priesthood of believers practice, all three men urged an organization-destroying independence.

“This question of organization,” Waggoner continued, “is a very simple thing. All there is to it is for each individual to give himself over to the Lord, and then the Lord will do with him just as he wants to (1899 GCB p. 86).

The next day Prescott, announced that “all politics and parliamentary procedures were from the devil,” who has only to dominate one mind to control the whole church. “There will be no officials here,” he exclaimed (ibid, pp 90-91). Jones at one point told conference members to stop asking questions of Waggoner and Prescott but to ask the Holy Spirit and the truth would “flow out.” The Spirit was thus to be the only coordinator (ibid, p. 91).

Their stress on individual access to God through Christ and personal dependence on the Spirit was vital. For “God has no grand children.” All are children with direct access. Their problem was that they negated the divinely appointed role of leadership and thus undermined human accountability.

Waggoner would resign his denominational position because of opposition to his efforts to de-organize; but Prescott later recognized this error, which placed him in direct opposition to Jones, his former mentor on both this count and his opposition to Panentheism. For though Jones never integrated Panentheism into his theology, he was influenced by its mysticism and intensely defended Kellogg over it.

Jones' key error? He assigned to the Spirit the role of leadership and organization that He assigns to us, a role to be carried out under the Spirit's training. For leadership with mutual accountability was not designed for power, as Jones claimed, but to help us learn humility and true love. Properly exercised, it cuts self-centeredness -- the nerve of sin. Organization is thus designed to develop the character of all. Whatever his role, each is to learn the lesson of subjection to one another and of honoring the gifts of the Spirit given to each:

[A]ll of you be subject one to another, and be clothed with humility: for God resists the proud, and gives grace to the humble. Humble yourselves under the mighty hand of God, that He may exalt you in due time (1 Pet 5:5-6).

Rather than the principle of mutual submission, Jones developed a non-Scriptural philosophy of personal independence based on a false doctrine that the Spirit is the only leader and organizer. He failed to consider the principles of God’s Word on which alone the church is to function. Christ Himself appointed Paul to apostleship, but sent to him the local church leader to pray for and to induct him into the church body. Barnabas, who had been commissioned by the Jerusalem committee, later called him into ministry at Antioch. He was then dedicated to ministry by the Antioch church, that was functioning under the direction of the Jerusalem conference to which he gave account throughout his life (Acts 15; 21:17-26).

Moreover, James functioned as “president” of the General Conference under the personal guidance of the Spirit, but was subject to the body over which he presided (president). Guided by the Spirit, all were “subject one to another,” none functioning independently. Thus, though called and ordained by Christ, Peter, most prominent of the twelve, was accountable to the same council as were all others (see Acts 10), and accepted public reproof by Paul (Gal 1).

Jones’ individualism caused him to trust onlyhis own judgment and left him open to confusion. Thinking he was led by the Spirit, he rejected admonitions not to join in Kellogg’s attempt to consolidate his own kingly power. Spicer reports his 1902 Tabernacle vestry echo of Kellogg as he over-literalized Isaiah to explain God’s vast form:

"'Hath measured the waters in the hollow of his hand' Open your hand as wide as you can, and hold it level, palm upwards. Note the depression in the middle of your hand. That is the hollow of your hand. Fill it with water and see how much it will hold without running over. And all the waters are measured in the hollow of God's hand as easily as those few drops of water lie in the hollow of your hand. Then if only his hand is so great that all waters lie in the hollow of it, how large is he himself? ...

"Meted out heaven with the span” [Isa 40:12]. The span is the measure from the tip of the thumb to the tip of the second finger. What is the compass of the heaven? Conceive it if you can. ... Then again, what is the size of that hand? No human mind can conceive of the compass of heaven. Then no human mind can conceive of the size of that span by which he meted out the heaven. And when no human mind could possibly conceive only the size of the hand, the reach of the span with which he meted out the heaven, how infinitely beyond all reach of human thought is any true conception of the form of God.

Spicer then explains Jones’ false assumption, that proved his “fatal flaw”:
The fatal error was the assumption that the prophet Isaiah [40:12] was endeavoring to impress us with the greatness of God's form. It is "the greatness of His might" (V 26) that the prophet is describing in these figures of speech. This philosophic view, set forth as the true one, was but repeating the ancient heathen philosophy of the Universe-God, sometimes thus given colossal members and parts, and again represented as an ether-like personality pervading all. The Hindu philosophy says: All this (universe) is Brahma." And Pike, an old Washington jurist, professor, and philosopher said of the Persian view: "It was thought the universe should be deemed an immense being." In the Egyptian and other philosophies, he says: "The universe was a living and animated being like man.... This was the Universe-God, which the ancients adored as supreme Cause and God of gods.... God, in the view of Pythagoras, was One, a single substance, whose continuous parts extend through all the universe. The world or universe was thus compared to man... Thus he made the universe a great intelligent being, like man--an immense deity." ... So came the idea of colossal form, such as we had pictured to us in the vestry of the Tabernacle in that Council of 1902.