Thought deceased after his encounter with the Devourer, Pythor suddenly resurfaced during the Nindroid war, allying with the Digital Overlord to seek revenge on the Ninja. Once again, his schemes were foiled after he was shrunken down by the shrinking pill and the Golden Master was destroyed. Afterwards, he was captured and sent to Kryptarium Prison.
After the Ninja realized Master Chen was after Pythor to finish the spell that would turn all the Cultiss into Anacondrai, the Ninja visited him in the prison, hiding him from Chen and the Cultists until he was ultimately captured. After completing the spell, he was left to be eaten by a swamp rat, but he escaped and ended up finding a spell in the Book of Spells that would allow them to summon the spirits of the Anacondrai Generals. After it was cast, Arcturus restored Pythor to his original size and he parted ways on understanding terms with the Ninja.