Let’s say that the whole “what Season 3 could/would’ve been” doesn’t affect this idea so we can ignore the Naugus thing, as Naugus left off on good terms with the Freedom Fighters so we have no reason to expect him to be evil.
So here’s how I see it: [Insert Clue Music and Tim Curry for Narration]
Shadow is the glowing eyes at the end of Season 2. Sometime just before Doomsday, Snively discovered a pod containing Shadow who promises Snively the chance to have Robotnik’s power and more. Snively agrees, and after the events of Doomsday gets Robotnik’s position as Rule of Robotropolis, though due to the Great Power Stones, there’s not much to rule. Shadow offers a power that overshadows the Great Power Stones, the Power of Chaos. Again Snively agrees.
Shadow then travels to the “Floating Island and Steals the Master Emerald. Knuckles only seeing it as a Hedgehog with great speed gives chase and ends up mistaking Sonic for Shadow, causing the two to fight. Using this to their advantage, Snively constructs a Robot Sonic (Metal) to distract Knuckles and a Robot Robotnik (Egg Robo) to distract the Freedom Fighters, while they head off to track down Lazaar’s Computer as they need it to extract the Chaos from the Master Emerald. The Robot Sonic is proven to be too good however, as it starts to develop pride and attitude like the real deal and begins to think it’s better than the real Sonic.
Sonic and Co are fighting off Robot Robotnik thinking he’s the real deal at first, however his tactics are much more….pathetic, as he’s really only a glorified SWATbot. But the main issue they have with beating him is that Knuckles keeps interfering trying to defeat Sonic. Finally the Robot Sonic interferes intending to beat Sonic, proving he’s the better hedgehog but is defeated by the combined forces of Sonic and Knuckles. This allows the Freedom Fighters the grounds they need to beat Robot Robotnik, discovering he too is nothing but a fake. After defeating him they find out Snively had created them as a distraction to hide his true purpose of finding Lazaar’s computer, which they find out is on an island not too far from the Main Lands (Flicky Island).
During this Story arc, Amy can be introduced as a new Freedom Fighter who has a hero worship of Sonic. Though she’ll play only a minor role for the time being.
Meanwhile Snively and Shadow find Lazaar and his guardian and using Shadow’s abilities defeat the duo. Lazaar is disposed of into the Void and they use his computer to drain the Master Emerald’s Power. The “good” energy of the Master Emerald is absorbed by the local wildlife while the “chaos” energy takes the form of chaos 0. However Chaos is mere fraction of his supposed power and Snively must track down mystical artifacts such as the Great Power Stones and the Time Stones to bring Chaos to full power. So he starts collecting the local wildlife (Flicky’s and the like) to use a power sources for his robots to find the other artifacts.
Sonic and Co, now being accompanied by Knuckles who believes Metal was the hedgehog who stole the Master Emerald, travel to the island to stop Snively, however by the time they arrive Snively is already gone. They do however destroy his base there and free the local wildlife from his harvesters.
While the Freedom Fighters are gone, Snively and Chaos find various power sources to fuel the creature’s appatite, including the Lower Mobius’s crystal and half of the rock….thing that makes Power rings. Snively also has captured quite a few of the powered creatures and harnessing that power has rebuilt Robotropolis back to full power.
When Chaos absorbs the half of the ...rock that makes power rings that Griff has, he is able to track the one in Knothole. Sonic and Co arrive just in time to fight Chaos but he has become too powerful for them to defeat. Snively takes their half of the rock that makes power rings (I know it had a name but I forgot) and take it back to Robotropolis. He intends to use it to create power rings for himself.
However, Chaos betrays him and absorbs the stone as well. Sonic and Sally are forced to used the Great Power Stones once again to stop him.
As this goes on, a subplot with the freedom Fighters plays out. Amy discovers the creatures being used to power Snively’s machines. Using her knowledge of mystic arts…
...no really. This is legitimately something she has in the game canon. She just never really uses it.
….she and some of the Freedom Fighters face off against the Robots being powered by the animals. Here they’ll befriend Gamma and defeat Zero. Upon releasing all the animals, the power forms to create the spirit of Tikal, an ancestor of Knuckles and friend of Chaos.
Sonic and Sally defeat Chaos, saving Robotropolis and with Tikal’s help Chaos’s power is restored to the Master Emerald.
However unlike the final battle against Doomsday, Sonic and Sally had to actually Fight Chaos, so rather than being left empowered, they’re left tired. Shadow uses this opportunity to steal the Great Power Stones, which he plans to use to power the Arc Laser. He reveals he used Snively to gain access to the stones so he could destroy mobius….
To be Continued.