The Silver Branch is the story of two cousins, Justin and Flavius, who are part of the Roman army in Britain in the third century. Justin is a surgeon and Flavius is trained as a soldier and they serve under Carasusius, the emperor of Britain and Gaul. Carasusius had rebelled against the Roman ruler Maximian who ultimately approves of Carasusius' role in Britain. Justin meets Flavius when appointed to the same military unit and they quickly discover that they are cousins. When the cousins accidentally learn of a plot to murder Carasusius by his finance minister, Allectus, they try to warn him but the emperor assigns them to duty on the Northern wall.

Thinking they have been disgraced by this assignment, Justin and Flavius soon learn from a local man named Evicoatos of the Spear, that the murder plot against Carasusius is real because he hears things among his people. Justin and Flavius realize that they must get to Gaul to alert the ruler Constantius about the plot to kill Carasusius but they meet a man named Paulinus who is organizing an effort against Allectus so Justin and Flavius decide to stay in Britain and help him. Justin and Flavius flee when Paulinus is murdered by Allectus' soldiers and they hide at their Aunt Honoria's home. While at her house they uncover a Roman eagle standard lost in an earlier campaign. Justin and Flavius use the eagle standard as a rallying icon to gather recruits and build a ragtag legion to fight against Allectus.

When Constantius finally arrives, Justin and Flavius and their legion join him in battle and defeat Allectus and his forces. Constantius pardons Justin and Flavius for abandoning their places on the North Wall and releases them from military service. Justin and Flavius, however, feel that Constantius is an emperor they could follow and decide to join his forces as they move northward into Britain.