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Möbius is a peaceful planet inhabitated by Mobians. It is the year 9012, and no humans are left except one: Dr. Ivo Robotnik. When an experiment goes wrong, Robotnik fuses with a rotten egg, becoming Eggman. He plans to take over Möbius, and only Sonic can stop him.
It starts by showing the year 2255 on Earth. Earth had been in war with the evil aliens know as the Xena for many years. The Xena were squid aliens who wore robotic exosuits. They used to be evil aliens with bodies, but a wizard turned them into squids. They have been in war with planets looking for a way to get their bodies back. They bombed Earth, transforming it to Möbius, and the animals evolved into Mobians.
Now it is the year 9012, and Möbius is full of advanced cities full of flying cars and futurtisic buildings. Everything is created by Dr. Robotnik, the last surviving human.
Sonic and Tails are running through Green Hill, as they go to their house. Their pet, Chilli Dog is waiting for them and barks as they enter. Tails has been working on an airplane known as the Tornado, and all he needs is an engine. Sonic says maybe Robotnik has the engine at the factory that they need. Tails gets ready to go, and they both run off to Robotnik Industries.
Later, Robotnik is in his lair experimenting to cure food allergies, to which Orbot replies is ridiculous. Robotnik has a rotten egg as a test subject. Robotnik is short, has a white lab coat, and a very small grey mustasche. He turns on the machine, making the rotten egg shock up, and fuse into Robotnik. He starts screaming as he transforms into Eggman. He grows fatter, his clothes get red, and his mustache turns brown and grows up. He then laughs evily as he goes to make blueprints for the Death Egg, a thing to robotize the entire planet. All he needs is the master emerald, and test subjects. He creates the Egg Carrier and flies off to New Mobe City.
When Sonic and Tails get to the factory and go in, they notice Robotnik is not there. Security robots are everywhere. Sonic and Tails notice this is strange, and run off to New Move City.
Later, in space, the Xena spaceship is flying around. Lord Overmind is sitting down watching TV laughing saying "that guy got hit in the head by a coconut!" A Xena Flier flies in and says there are massive amounts of energy emitting from a planet light years away. Lord Overmind looks on his screen to see Möbius, and the energy came from Eggman's food allergy machine. They look around and see Tails. Their eyes light up yelling. "The legendary Kitsune!!! The only one who can bring our bodies back..... Set a course for MOBIUS!!!!"
Back on Möbius, robots start invading the city, destroying everything, kkidnapping Mobians in cages. The Mobians scream as they are caged, cars are crashing everywhere. All of the sudden, Sonic comes out of nowhere. He is puzzled to see Robotnik Inc. Robots attacking the city.
He starts dashing and destroying robots, also doing homing attacks on them. He picks up a ring and does a giant dash to them. Tails comes in with the Tornado, which he had found an engine to. He starts firing at the robots. Eggman comes in the Egg Crusher (Like on the start of Sonic Unleashed.) He starts laughing as he says he plans to robotize the entire world, and nobody can stop him. He says he plans on using these Mobians as test subjects. Tails then throws the Chaos Emeralds at Sonic, and he transforms to Super Sonic. Sonic starts chasing Eggman on rooftops as Tails frees the captured Mobians.
Sonic destroys the Egg Crusher, and transforms back to regular Sonic. Eggman laughs as the Egg Mobile flies up, carrying a cage with a rabbit Mobian inside. It is Bunnie Rabbot. Eggman presses a button, and the Egg Carrier appears over the city. A claw comes down from it and picks up the Egg Mobile. Sonic tries to get Eggman, but it goes up too fast. The Egg Carrier teleports at warp speed.
Sonic looks up and says, "this isn't over... Eggman." Tails flies up to him in the Tornado and Sonic gets in, and tells Tails to chase after Eggman. Chilli Dog barks as they fly away.
It has been 2 years since then, and Sonic and Tails have traveled the world searching for Eggman. Right now they are flying over Twilight Forest, a place close to Spagonia. They land in the forest and Sonic says they should camp here for the night. Sonic, Tails, and Chilli automatically fall asleep. When they're asleep, a shadowy figure appears with a sack, and kidnap the three.
In space, the Xena are almost to Möbius, and the Xena are having a giant party, celebrating they'll have their bodies back soon.
The next morning, Sonic wakes up to see the Freedom Fighters standing over him and watching him. He jumps up and