Brotherhood of the Scroll is the story of a small group of Jewish patriots intent on helping their nation navigate the dangers of a turbulent international scene in the light of God's revealed will. Babylon and Egypt stand as the two military superpowers of the day, with Tyre acting behind the scenes as an economic powerhouse. Spanning the period 605 B.C. to 586 B.C., the challenge for Jeremiah, Daniel and their companions is to preserve the faith of their people while seeking the fulfillment of prophecy amidst international intrigue and war. The book is divided into three parts.

Part I: The Prophecy of the Scroll

Brotherhood of the Scroll opens with the prophet Jeremiah delivering a sermon in the Temple of Solomon, predicting that Judah will be carried into exile to Babylon for 70 years. Forced into hiding from the evil king Jehoiakim, Jeremiah forms the "Brotherhood of the Scroll" which will attempt to give hope to the Jews and point the way of redemption for their people.

Three subplots are also introduced in this section. The first is a plan by the King of Tyre to form a league of nations allied with Egypt to restore a long-buried canal linking the Nile River to the Red Sea. Nebuchadnezzar becomes aware of the canal project and plots to prevent Egypt from completing it.

The second subplot is a plan by the Chief Priest of Babylon, Hamon, to wrest the kingship of Babylon from Nebuchadnezzar. All that stands in his way is a young Hebrew exile named Daniel, who has been made a Magi in Nebuchadnezzar's court. Hamon realizes that Daniel must be eliminated if his plan is to succeed.

Third, the reader is introduced to the nation of Kush, which lay to the south of Egypt. For one hundred years, the kings of Kush ruled Egypt. Now a fourth-rate power, the Priests of Amun harbor desires to regain their former glory.

Part II: The Judgement of the Scroll

In this section of the novel, the geopolitical struggles between Babylon and Egypt are further developed. Nebuchadnezzar realizes that to win victory against Egypt, he must open a second military front against his enemy, and so begins a long term strategy to gain the assistance of Kush. A clandestine war of assassination and bribery is played out between the two superpowers as Babylon compete for world dominance. seeks to gain the aid of the Priests of Amun, while Egypt enlists the help of Aspelta, the brother of the King of Kush.

Following Babylon's defeat at Migdol, the economic strain of supporting Nebuchadnezzar's military campaigns creates internal dissension in Babylon. Through his network of spies, Troas learns of Hamon's desire to win the throne of Babylon, and seeks to exploit that information. In exchange for agreeing to help hunt down Jeremiah, Troas convinces Jehoiakim to have his people in Babylon assassinate Daniel. Taking advantage of Hamon's thirst for power, Troas's spies gain the Chief Priest's help. However, Nebuchadnezzar has a dream which Daniel volunteers to interpret. In an effort to kill Daniel before he can interpret the dream, the timetable for the assassination is accelerated. Naaman thwarts the attempted assassination, and suspects (but cannot prove) Hamon's involvement. Naaman forces Timnah to turn against Hamon and gain the proof he needs.

Part III: The Promise of the Scroll

In this last section, the three subplots are tied together to bring the story to a close. First, Daniel survives Hamon's plot to have him thrown into the lions' den, and with Timnah's help, uncovers Hamon's plot to depose Nebuchadnezzar and take the throne of Babylon.

Second, Nebuchadnezzar learns of the creation of the League and of Zedekiah's role, and lays plans to sack Jerusalem. Zedekiah, in an attempt to ward off disaster, seeks the help of Jeremiah, who implores him to free the Jewish slaves as required by the Lord's commandments regarding the Year of Jubilee. Under the prompting of Troas, Zedekiah does so, only to renege on his word when an Egyptian army appears and draws off the Babylonian invaders.

Third, Babylon is successful in causing the fall of the Egyptian puppet government in Kush, which then begins to invade southern Egypt. Pharaoh learns of this just when he is preparing to do battle against the Babylonian army in southern Judah, and must lead his army back to Egypt to face Kush. Naaman and Troas meet in single combat when a Greek mercenary unit under the command of Troas is cut off from the main Egyptian force, and does not learn of the order to withdraw from the area near Jerusalem.

With Jerusalem in flames, the Temple destroyed, and Zedekiah dead, the last of three exile waves is taken into captivity to Babylon. But all is not lost, for Daniel, guided by the prophecy of Isaiah 44:28, has learned the promise of the Scroll of Isaiah. Daniel now knows that the Lord will deliver His people just as He promised.