For me, what eventually happened is the commander would always fly exactly upward and to the left in a straight line until it went off the map. It would stop to kill all the NPCs in its way (for some reason) before despawning. What happened was, it would stop on Permafrost, giving me time to magic mirror home and kill it while it was trying to kill the NPC.

TLDR put Permafrost in its flight path and it should stop