After the events of Sonic Adventure 2, Mobius was once at peace again. Dr. Robotnik has realised his mistakes and had gone back to his secret laboratory to create a ship where he could live at peace away from Mobius so he would never get the urge to destroy something again.
Meanwhile the freedom fighters were eating supper at the Emerald Hill hideout, outside by the camp fire. Sonic looked in the sky and thought about how much he missed Shadow after he died as he never got to know him better. Sonic only knew Shadow as an obsessed hedgehog, carrying out Dr. Robotnik’s orders. He only became to know him better after he realised the words of Maria Robotnik, his creator. This is when Shadow realisd he must keep Mobius at peace and not destroy anything through anger. Sonic knew that Shadow was a freedom fighter at heart but he will never know since he burned up in Mobius’ atmosphere after using the Chaos Control to stop the Ark from careering into Mobius.
But little did Sonic know, Shadow’s charred remains were floating in the megamack (a type of toxic sludge) in the Chemical Plant Zone. Because of this they were preserved perfectly, no blood was lost and no decay had taken place.
It was at this moment that Dr. Robotnik’s old right-hand man, Grimer (who was thrown out of Dr. Robotnik’s lair because he was plotting against him) happened to walk across the path next to a lake of megamack and see an arm bob above the surface. Grimer called to see if there was any life but the megamack is so poisonous, the fumes would kill anyone instantly. So he quickly ran back to his run-down lair to get a device that looks like a small, mechanical crane arm to pick the body out of the megamack. When Grimer got Shadow’s remains from the megamack he realised who it was… this got Grimer scheming. Grimer thought that using Shadow he could destroy Dr. Robotnik and take over Mobius! So Grimer took the burnt Shadow to his lair to start reconstructing him using badnik technology…
