Board Thread:General Discussion/@comment-2055856-20160708073759/@comment-679780-20160711170453

Luma.dash wrote: 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.

However, even if this is true. The whole timeline rebooted after Solaris' destruction. So, this is no longer canon. Shadow saw his imprisoned self in Flame Core. https://youtu.be/gHdxCSaAHig?t=266

It could be possible Shadow was accused as the murderer of Sonic due to his similarities with Mephiles.