After the war began, he stumbled across a group of Vahnatai from the Olgai tribe. Sixus secretly tried to convince them that Avernum was not responsible for the theft of their Crystal Souls. As this task was later accomplished by the Empire War Heroes, it seems he was not successful.
Nonetheless, the Empire discovered what he was doing and tried to have him killed. First he was attacked by a company of Avernite soldiers. He survived, and fled with four apprentices, taking numerous war documents with him to a tower he built across the river, northeast of Almaria. Almarian officials thought he was delusionally paranoid and hadn't been attacked. As it turned out, he had been attacked, but the soldiers had been charmed by the Empire. And he was right to be paranoid, for the Empire sent more soldiers to attack his new hiding place. Sixus eventually fled to another, unknown location with his apprentices. Beyond that, his fate is unknown.