Three years after Cipher was once again thwarted by Michael, a young man begins his journey through Orre, now seeing more signs of wild Pokemon. However, his journey is put into jeopardy as signs of the existence of Cipher begin to emerge. Together with his two companions, and his Pokemon, Hakins will begin his quest to uproot Cipher once and for all.

Julius wakes up with no sense of where he is – his arms and legs are bound tightly with vines, and he's suspended in the air. His pokemon are nowhere to be found. A woman he's never met begins to interrogate him – she accuses him of trying to steal from her. Julius pleads his ignorance, but as the terrible fate beneath him is revealed, things get desperate.