The Second Installment of the Fifth Course of Punishment was described to Daniel as the time when the city of Jerusalem would be restored, but that "the street shall be built again, and the wall, even in troublous times." This would be done under the reign of the Medo-Persian empire, the second Gentile dominion that would hold sway over Israel during the Fifth Course of Punishment. The books of Ezra, Nehemiah, and Esther record Israel's history during the Second Installment.

In Ezra emphasis is laid upon the rebuilding of the temple in Jerusalem. Ezra was a priest who responded to the command to return to the land.

Nehemiah especially records the rebuilding of Jerusalem. Ezra, Nehemiah, and Esther emphasize the "troublous times" Israel experienced during this Second Installment, as Satan opposed Israel's re-admittance to their land. They were still his "lawful captive" and faced his opposition both outside the land and within.

At the conclusion of the Second Installment Israel began to experience a very unique form of chastisement belonging to the Fifth Course of Punishment. During the Third Installment God went silent to Israel. For a period of about 400 years God said nothing to them. They had no prophets functioning and God gave no evidence that they were His people. They experienced a "famine of hearing of the words of the LORD." Haggai, Zechariah, and Malachi functioned during the Second Installment and were the last prophets to Israel before God went silent. The blank page in the Bible between Malachi and Matthew ought to be thought of as representing the Third Installment.

Because of the nature of the Third Installment, there is no confusion or doubt regarding what to do with the books called the Apocrypha written during this time. Since God was silent, they are not the word of God. Therefore, they are not to be included in the Bible.