Board Thread:General Discussion/@comment-2055856-20160708073759/@comment-24014422-20160711120732

According to Mephiles, Shadow was hunt down by a re-programmed E-123 Omega after the humans feared that Shadow would be an enemy for them after Iblis' crisis. Whether Mephiles was lieing at that time to gain Shadow's trust or not, is unknown. But you can see the cutscene just before Mephiles phase 1 boss, and the cutscene after Shadow's Wave Ocean for more details