The season two finale,
The Doomsday Project (1994) (which was also the final episode), ended with a cliffhanger indicating that Snively was going to take over as the new primary villain on the show starting in season three, and he also revealed that he had a new partner, who was only indicated by red, glowing eyes. Contrary to popular belief that these eyes belonged to Knuckles or Metal Sonic, writer
Ben Hurst revealed that they actually belonged to Naugus. He explained that the plans for the third season were: Snively tries to retake control of Robotropolis, but ultimately fails. On the verge of losing it all to the Freedom Fighters, he turns to
The Void (1994), where Naugus is busy torturing Robotnik. Snively frees Naugus, and in the process also frees Robotnik and King Acorn. Naugus assumes control, and starts his new command by trying to lure Sally into capture with the King as bait. Robotnik becomes Naugus' lackey. And Snively, now reduced to a simpering nobody, defects to the Freedom Fighters. Hurst went on later to say that more developments would have come along between the relationship of Sonic and Tails, coming a little closer to the game relationship it strayed so far away from. Sooner on down the line in possible future episodes we would also have learned of the origins of Robotnik and Snively.