Nephi made two sets of plates, one large and one small. The small plates contain the sacred things and the large plates contain the more detailed secular history, including the reigns of kings and wars and contentions.
So, you can see that the Book of Mormon was not just one set of plates but was actually made up of many groups of records, which is best understood through an illustration. See the diagram below.
Source: "Mormon Plates and Records", http://www.lightplanet.com/mormons/book_of_mormon/plates.html
Even though a picture is worth a thousand words, some explanation is helpful here. It is easiest to simply quote here from the "Brief Explanation" page at the front of the Book of Mormon.
The Book of Mormon is a sacred record of peoples in ancient America, and was engraved upon sheets of metal. Four kinds of metal record plates are spoken of in the book itself:
The Book of Mormon comprises fifteen main parts or divisions, known, with one exception, as books, each designated by the name of its principal author. The first portion (the first six books, ending with Omni) is a translation from the Small Plates of Nephi. Between books of Omni and Mosiah is an insert called The Words of Mormon. This insert connects the record engraved on the Small Plates with Mormon’s abridgment of the Large Plates.
- The Plates of Nephi, which were of two kinds: the Small Plates and the Large Plates. The former were more particularly devoted to the spiritual matters and the ministry and teachings of the prophets, while the latter were occupied mostly by a secular history of the peoples concerned (1 Nephi 9: 2-4). From the time of Mosiah, however, the large plates also included items of major spiritual importance.
- The Plates of Mormon, which consist of an abridgment by Mormon from the Large Plates of Nephi, with many commentaries. These plates also contained a continuation of the history by Mormon and additions by his son Moroni.
- The Plates of Ether, which present a history of the Jaredites. This record was abridged by Moroni, who inserted comments of his own and incorporated the record with the general history under the title “Book of Ether.”
- The Plates of Brass brought by the people of Lehi from Jerusalem in 600 B.C. These contained “the five books of Moses, . . . And also a record of the Jews from the beginning, . . . down to the commencement of the reign of Zedekiah, king of Judah; And also the prophecies of the holy prophets” (1 Nephi 5: 11-13). Many quotations from these plates, citing Isaiah and other biblical and nonbiblical prophets, appear in the Book of Mormon.The longest portion, from Mosiah to Mormon, chapter 7, inclusive, is a translation of Mormon’s abridgment of the Large Plates of Nephi. The concluding portion, from Mormon, chapter 8, to the end to the volume, was engraved by Mormon’s son Moroni, who, after finishing the record of his father’s life, made an abridgment of the Jaredite record (as the Book of Ether) and later added the parts known as the Book of Moroni.In or about the year A.D. 421, Moroni, the last of the Nephite prophet-historians, sealed the sacred record and hid it up unto the Lord, to be brought forth in the latter days, as predicted by the voice of God through his ancient prophets. In A.D. 1823, this same Moroni, then a resurrected personage, visited the Prophet Joseph Smith and subsequently delivered the engraved plates to him.
These first 116 translated pages represented the Large Plates of Nephi and contained the book of Nephi's father, Lehi (see diagram above; also see Lesson 14: “For a Wise Purpose”, Book of Mormon Gospel Doctrine Teacher’s Manual, (1999), 61.)
Joseph was commanded by the Lord to not re-translate the missing pages because the conspiracy that was afoot was to alter the original manuscript so that his detractors could "prove" him to be a false prophet when the two translations did not agree. The Lord then revealed to a penitent Joseph that He had seen this coming centuries before (D&C 10:8–14) and had ensured that what was lost on the 116 pages would be duplicated in the translation from the Small Plates of Nephi. This record is what is now found in the books of 1 Nephi through Omni.