Historical analysis: Verse 28 contains the scriptural basis of the eighth article of faith's qualification that we believe the Bible "as far as it is translated correctly." This set of verses is also a part of the fuel which feeds the folk tradition that there have been conscious, and at times malicious alterations of what we have as the Biblical text. This latter assertion has very little evidence to support it, for all that it has been widely held frequently circulated with various supporting "facts."
The story of the development and preservation of Biblical texts is well known, and there are sufficient copies of most texts to allow scholars to provide reasonable reconstructions of what may or may not have been added into the texts. To be sure, scholarship has invented its own agenda in this arena, and some of the modern work on reconstruction has done more to "take away precious parts" than all previous scribes. Nevertheless, the overwhelming evidence is that the scriptures as we have them have had a reasonably faithful transmission, and that there is little evidence which can be amassed for the "intentional alteration" idea.
What then are these verses talking about? It is important to remember that these verses are precisely in the same prophetic vein as the discussion of the foundation of the United States. The historical reality of the foundation of the United States as a nation independent required both the war of Independence, and the war of 1812, but only a single conflict is mentioned. The nature of this type of vision is one of condensation of detail into the essential information. The essential information of the establishment of the United States is more important that the historical details which led to it.
Likewise, these verses are setting up an important fact which is much more important than the nature of the Biblical text. To understand the import of these verses, we need to return to verses 25 and 25:
"24 And the angel of the Lord said unto me: Thou hast beheld that the book proceeded forth from the mouth of a Jew; and when it proceeded forth from the mouth of a Jew it contained the fulness of the gospel of the Lord, of whom the twelve apostles bear record; and they bear record according to the truth which is in the Lamb of God.
25 Wherefore, these things go forth from the Jews in purity unto the Gentiles, according to the truth which is in God."
The first important clue that this is a condensation of reality comes in verse 24 where the angel notes that the book proceeds from the mouth of a Jew. Note the singular. This is a clear inaccuracy. Anyone familiar at all with the Bible, and certainly Nephi familiar with the brass plates to which the Bible had been compared, would know that the there are multiple authors of what has been collected into the Bible. The singular is used because the details of the reality are not important. What is important is the source, and the subsequent history of that source. For the angel, the essential data required about the source is first, that it comes from the chosen people, to whom the covenants and promises have been make, and second, that it is a true record (which is the function of verse 25).
Note the nature of the change that occurs in verses 26 and 27:
"26 And after they go forth by the hand of the twelve apostles of the Lamb, from the Jews unto the Gentiles, thou seest the formation of a great and abominable church, which is most abominable above all other churches; for behold, they have taken away from the gospel of the Lamb many parts which are plain and most precious; and also many covenants of the Lord have they taken away.
27 And all this have they done that they might pervert the right ways of the Lord, that they might blind the eyes and harden the hearts of the children of men."
The true record, with the true witness of the twelve apostles of the Lamb, encounters the great and abominable church. It is after this encounter that plain and precious parts are taken away. Note that in addition to plain and precious parts of the book, there are also covenants that have been taken away? What is happening here?
When it was fashionable to equate the great and abominable church with the Roman Catholic church, these verses would feed the folklore stories of hidden manuscripts in the vaults of the Vatican with heavy deletions. These things do not exist, and should be relegated to the archives of folklore.
What is really happening in these verses is the condensation of the great apostasy into a few short verses, and defined by its most salient effect, the diminished understanding of the gospel as contained in the Bible, and the loss of covenants. As with the wars, the prophetic vision is not attempting to discuss particular events, but to describe the general occurrences which lead to the ultimate redemptive vision of Nephi's people. The essential reality is the apostasy, not the textual transmission of the Bible itself.
Thus in verse 28:
"28 Wherefore, thou seest that after the book hath gone forth through the hands of the great and abominable church, that there are many plain and precious things taken away from the book, which is the book of the Lamb of God."
The plain and precious things are taken away from the book directly through the manipulation of the great and abominable church. From an historical standpoint, this involves a long process, including the early Hellenization of the Jewish Christian movement. The angel is describing the result of a long process, not specific details.