Shadow stared at the pile of rubble, content with his actions, and completely unaware of what he had done. As he turned away from the smoldering ashes, he couldn't help but feel something was wrong. He couldn't tell what, but he felt guilty at his actions, like he had done something horrible. This thought faded away as Eggman's voice came in through a transmitter in his ear. "Shadow, is your task complete yet?"
"Yes, Sonic is...eliminated." Shadow felt slightly sad as he uttered that sentence.
"Good. Now come back to the base. I would like to give you some more upgrades."
"Yes sir." Shadow bolted off towards the base, still feeling slightly guilty.
He poked his head out and took a look around. Nothing left. He crawled out, having to take extra care as to damage himself further. He pushed away some rubble as he made his way out. Sonic was lucky to remember about the secret, underground room Tails had installed. The blast still affected him, greatly so. It threw him down to the ground, knocked several things on the shelves (and the shelves) off, and the heat nearly cooked him alive. The initial explosion blew the trapdoor off, but the only after effects was fire seeping in, which was easily out out with the fire extinguisher on the wall. Sonic sprayed out several of the fires that were in his way, as he surfaced from the rubble. He was finally able to stand up, as he crawled out of the pile, but immediately fell over due to a pain in his bad leg.
He looked at it and noticed the device was damaged. He couldn't even stand the pain of crawling anymore. The only thing he could do was lay there and wait for Tails and the others to return. As he lay on the ground, feeling the heat from what was left of Tails' Workshop, he remembered what Shadow had said. He talked about something called the Ark, which involved GUN. Sonic didn't know what this was, but he knew it must have been something that had been pretty bad for Shadow to try to kill him for being involved. Then a realization came to him. Something that hurt him more than his physical pain. Shadow had tried to KILL him. The same person that loved him honestly wanted Sonic to die, and that scared Sonic.