The 1888 message of righteousness by faith was parallel to and consistent with the unique Seventh-day Adventist truth of the cleansing of the heavenly sanctuary. Jones’ and Waggoner’s outstanding views on this subject can be found all through their published writings: Jones’ understanding of the cleansing of the sanctuary is implicit throughout his 1893 studies on "The Third Angel’s Message." Here again was something beyond the ken of the 16th century Reformers, or even of Moody or Spurgeon. As early as the Minneapolis Conference itself, Ellen White began to sense the relation of the Jones-Waggoner message to this grand truth. And shortly afterwards, we find her linking the message of justification and righteousness by faith with the work of the great High Priest in His "closing work of atonement" in the Most Holy Apartment. A study of her messages to the ministers and the church at large after 1888 reveals a preoccupation with this aspect of their message. Here was a work to be accomplished that had never yet been done in human history. She was excited; if the ministers and people would follow Christ by faith in His closing work, the coming of the Lord would be very soon.
Until the turn of the century, Jones and Waggoner were clear in their grasp of the sanctuary truth, and Ellen White supported their published view of its ethical and spiritual implication. Ellen White’s understanding of the cleansing of the sanctuary broadened during the 1888 interest. She frequently related the Laodicean message to the work of our great High Priest, and correlated the work in the sanctuary in heaven with preparing "the people of God to stand in the great day of God". The High Priest can never cleanse the heavenly sanctuary of the sins of His people until He can first cleanse them from the human heart; the books of heaven merely record or mirror the state of His people’s character on earth. The how of the sanctuary cleansing is therefore closely related to the true message of righteousness by faith."
Seen in this light, there emerge two streams of teaching on "righteousness by faith": (1) the genuine which has its source in the ministry of Christ in the Most Holy Apartment and (2) the counterfeit which has its source in the one who is seen "trying to carry on the work of God" in the apartment "Jesus has left." He deceives those "professed Christians" who are either ignorant of or who neglect the truth of the cleansing of the sanctuary:
I saw that as the Jews crucified Jesus, so the nominal churches had crucified these messages, and therefore they have no knowledge of the way into the Most Holy, and they cannot be benefitted by the intercession of Jesus there. Like the Jews, who offered their useless sacrifices, they offer up their useless prayers to the apartment which Jesus has left; and Satan, pleased with the deception, assumes a religious character, and leads the minds of these professed Christians to himself, working with his power, his signs, and lying wonders, to fasten them in his snare. Satan would breathe upon them an unholy influence; in it there was light and much power, but no sweet love, joy and peace. Satan’s object was to keep them deceived, and to draw back and deceive God’s children. I saw one after another leave the company who were praying to Jesus in the Holiest, and go and join those before the throne [of the first apartment where Satan carries on], and they at once received the unholy influence of Satan.