So it all starts out after Sonic and Shadow have defeated the FinalHazard in SA2. Sonic manages to save Shadow before he falls to Mobius and brought him back to Space Colony Arc.
"You think they did it?" Knuckles said.
Everyone turned around as they heard the doors open revealing Sonic and an exhausted Shadow.
"Sonic!" Amy and Tails said.
"And Shadow!" Eggman said.
"Is he okay?" Rouge asked.
"He's a tough guy! He'll be fine! We just need to patch him up a little." Sonic replied.
Shadow opened his eyes weakly as he smiled.
"Thanks for saving me, Sonic." Shadow said quietly.
"You're welcome, Shadow." Sonic said. "C'mon guys. Let's go home."
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(This is the comic where I got the idea. But I don't own it)
After that, during the events of Sonic Unleashed with Silver, in his time period the world is falling apart thanks to Dark Gaia. So he went back in time to find Sonic for help. Shadow also tagged along as they went to stop Eggman. When they thought they stopped him Silver knew they fell right into a trap. Thankfully he managed to get the button before Eggman pressed it. Shadow was about to arrest him, but Eggman blasted him in the head and he got the ability to see into the future. But Eggman still able to spring his trap. Along with blowing up the world, Eggman extracted Shadow and Silver's powers. He also tried getting Sonic's dark powers but it failed. The hedgehog's powers are stored in prototype emerald copies.
Eggman used them to power his new machines along with what he currently had. He used Shadow's powers to charge the Egg Beetle, Silver's powers for the Egg Devil Ray, and both for the Egg Lancer. After that battle Eggman lost both of the emerald prototypes containing Shadow and Silver's powers, and Sonic then has them.
During the Eggdragoon fight Sonic broke Shadow and Silver free from the mech, since Eggman knew Sonic had their powers. Shadow and Silver crushed the emeralds containing their powers as they got their abilities back.
Sonic, Shadow, and Silver all finished off Eggman, and then finished Dark Gaia all together with Chip/Light Gaia.
And that is all of what happened to Shadow before Return of Darkness.
