Chapter 11: The Ultimate Life Form
Eggman moved a full assault on Prison Island with only himself and his two robot assistants. He eventually retrieved what he was looking for and managed to escape with it.
Several days later a Chaos Emerald was stolen from a museum, a security tape revealed the intruder to be Sonic the Hedgehog. Everyone was shocked and also started blaming the blue hedgehog for aiding Eggman in penetrating Prison Island. Sonic was eventually captured by GUN. Sonic escaped, claiming he was innocent. While running from GUN robots, Sonic runs into a robot stronger than the other. Sonic defeated the machine, and when he did, a green glow appeared at the head of the fallen robot, when the glow faded, there stood a jet black hedgehog with red streaks on his hair like head quills who had a slight resemblance to Sonic. This explained the video footage of the hedgehog stealing a Chaos Emerald, it was that black hedgehog, the video was just to dark to see the difference. Sonic and this black hedgehog fought, but Sonic was outmatched in strength, skill and even speed. The black hedgehog revealed his name to be Shadow the Hedgehog, the ultimate life form created by Gerald Robotnick. Shadow had been beating Sonic by using Chaos Control, but no one noticed since Shadow only had one Chaos Emerald.
At the end of the fight, GUN showed up and Shadow left, leaving Sonic with the blame once again. Sonic decided just to turn himself in because he heard he was going to be taken to Prison Island. He hoped he would find out something about Shadow there since that's where Eggman found Shadow.
Eggman and Shadow were working together to recover the Chaos Emeralds to power the Eclipse Cannon, the ultimate weapon on a the secret space colony, ARK. Rouge the bat also helped them recover Chaos Emeralds, but she was actually a spy sent by the president.
Rouge and Shadow were sent to recover the Chaos Emeralds on Prison Island when Sonic was there. They would steal the Emeralds and destroy Prison Island with a bomb placed in the ammunition bay. The plan was ruined when Rouge was locked inside the room with the bomb. Shadow was unable to help because he was fighting Sonic who was freed by his friend Amy and her giant hammer. When Sonic heard about the bomb he ran to warn everyone. The human Chris then saw Shadow just before he used Chaos Control, he charged at Shadow and ended up teleporting with him. Shadow then saved Rouge and Chris, teleporting them to Space Colony ARK.
After many battles with Sonic, Eggman finally recovered all the Chaos Emeralds and placed them in the power source for the Eclipse Cannon. Fortunately the cannon was destroyed by Sonic and Shadow during their fight and it was unable to fire. Suddenly an old recording of Professor Gerald started playing and the Chaos Emeralds were sealed off. The recording was Gerald's plan to destroy the planet by ramming it with the entire space colony. The Chaos Emeralds turned the Eclipse Cannon into a megabomb that would detonate on impact with the planet. The emeralds were also powering the engines pushing them towards the planet.
Chris was in another room hoping Sonic would get there in time. Shadow overheard him and said not to get his hopes up. This was apparently Shadow's plan from the start. Shadow was taking revenge on the planet for taking Maria away from him. When Shadow was released 50 years ago, GUN came to shut down Project: Shadow and when they saw Shadow with Maria they chased them. In the end Maria was shot and killed in front of Shadow who was sent in a pod towards the planet. Since then Shadow swore he'd avenge Maria's death.
Chris convinced Shadow that Maria wouldn't want Shadow to do this, she'd want him to help people and be their friend. Shadow rushed to help Sonic and the others as they entered the room with the Chaos Emeralds. When they entered the room, the Biolizard was set free and doing everything it could to ensure the collision happened. Shadow was able to hold it off while Knuckles used the Master Emerald to drain the Chaos Emeralds of their power. Suddenly the Biolizard used Chaos Control to fuse with the the ARK. In their last effort Sonic and Shadow restored the emeralds power and transformed to their super forms. Sonic and Shadow fought the Biolizard before it could pull the ARK to close to the planet. The two hedgehogs used Chaos Control to place the colony back into a stable orbit. Unfortunately Shadow used up all the energy he had, the only thing left was a power ring Sonic found and gave to Chris.
As Sonic and his friends left the observation room Sonic stayed behind and looked out into space and said "Sayonara, Shadow the Hedgehog."