After establishing good fruit in the original root, the Lord of the vineyard visited the scattered branches in "the nethermost part of the vineyard." (5: 19-20; see also 3 Ne. 16: 1-3.) The Lord of the vineyard was satisfied that in each of the places where the natural branches were scattered, good fruit had returned. (5: 20, see also 2 Ne. 29: 12.)
Whether it was the "poorest spot in all the land of the vineyard" or another place "poorer than the first" it did not matter. The result was good fruit. (5: 20-21; 23.) The servant was dismayed at the locations to which the Lord had taken the scattered branches. In perplexity he inquired: "How comest thou hither to plant this tree, or this branch of the tree? For behold, it was the poorest spot...?" (5: 21.) The servant was surprised to know the Lord of the vineyard would go to visit these poor places. It seemed beneath the Lord to have ministered in such humble, far flung lands, among such woebegotten peoples. But the Lord has "descended below them all" (D&C 122: 7-8) and found no indignity in visiting with such humble people in diminished circumstances. It may well have been because of the difficulty of the circumstances that fruit was produced. (Alma 32: 12-13.)
As if to confirm that difficulties are a blessing to His vine, when they get to the "good spot of ground," the transplanted branches have produced conflicting fruit. In this most chosen land of all, the brothers were divided, and fought in continual ethnic-cultural-religious warfare for generations between themselves. Part of these branches produced good fruit, but part was corrupt and wild. (5: 25.) Although this was the best spot in the vineyard, and although the Lord of the vineyard had "nourished this tree like unto the others" it was still half corrupt. (Id.) This tree required pruning.
The Lord decided to "Pluck off the branches that have not brought forth good fruit, and cast them into the fire." (5: 26.) Accordingly, nature itself removed the branches: "And thus the face of the whole earth became deformed, because of the tempests, and the thunderings, and the lightnings, and the quaking of the earth. And behold, the rocks were rent in twain; they were broken up upon the face of the whole earth, insomuch that they were found in broken fragments, and in seams and in cracks, upon all the face of the land. And it came to pass that when the thunderings, and the lightnings, and the storm, and the tempest, and the quakings of the earth did cease—for behold, they did last for about the space of three hours; and it was said by some that the time was greater; nevertheless, all these great and terrible things were done in about the space of three hours—and then behold, there was darkness upon the face of the land." (3 Ne. 8: 17-19.)
The pruning then, like the Lord of the vineyard's pruning at any time, was targeted and specific. It is designed to remove only the branches worthy of destruction. The righteous do not need to fear. Those who reject the prophets sent to them, reject the prophets' message, and give no heed to the prophets, need to fear. (3 Ne. 10: 12-14.) The message of Jacob comes full circle. He returns to his earlier theme, when he promised the righteous they would be spared. (See 2 Ne. 6: 18, and the prior post Nephi's Brother Jacob, Part 7.) He is consistent.