Author's Notes:

Obligatory disclaimer, I don't own the Sonic world + characters (big surprise there, huh?)

This is one of the many random ideas that finally made it's way to paper. Figuratively speaking.
As with most of my stories, it's got a vague plan, and most of it is being made up as I go along. Somehow, despite being a totally illogical way of doing things, it always seems to turn out better for me that way.
I'm not sure if this one will actually be finished though. It may be a one off idea that doesn't really go anywhere for me.
Anyway, enough from me. See what you think.

Amy hammered on the sides of the wall surrounding her. She could only watch and hope.
Sonic was surrounded by SWATbots, and some unusual looking ones at that.
In one of his usual floating pods, Robotnic sat taunting him.
As usual, Sonic showed no sign of concern, making ready to destroy yet more of the doctor's creations.
She couldn't hear what was said, or what happened, but it looked like Sonic had attacked one of them, which had something on it that reacted to his contact.
Sonic collapsed to the ground, unconscious. The walls of the container were retracted, and she went immediately to him.
He was alive, and unharmed. Just not awake.
"What've you done to him?" she screamed at Robotnic.
"Oh, nothing much... he'll just be sleeping away while I put my latest plan into action! This time he won't be able to stop me. SWATbots! Retreat! Our work here is done."

Sonic was perplexed. There he was, laying on the hospital bed with Amy stood over him. And here he was, stood beside her, apparently completely invisible to everyone. He'd followed her from outside Eggman's base to here, trying to make sense of it. He wasn't dead, just in coma, the doctors had said. So what was this, an out of body experience?
He couldn't seem to interact with anything, except to pass through it. Floors seemed to be the exception, but only when he wanted them to. He hadn't tried the same on people – every time someone passed near him, he was sure there was some kind of force pulling on him. Only his own body and Amy didn't seem to do it. He didn't want to find out what would happen if someone walked through him. Not yet, anyway.
As an experiment, he'd tried overlapping his own body, but it hadn't made a difference. When he got up again, he was still separate from it.
"C'mon Sonic," Amy murmured. "Wake up."
"I would, if I knew how," he replied, even though she couldn't hear him. He'd tried shouting, yelling, screaming – no one heard anything. "I guess I'm not going anywhere. Amy probably won't leave me."
"I won't leave you. Not until you wake up."
"Yeah, thanks for that. I just said that. Guess I don't have anything better to do than wait." Someone pushed a trolley right through him. He stepped clear before they did too. "Maybe I should take advantage of all this?" He grinned. "I wonder what Shadow's up to?"
He jumped through the floors, coming to the ground floor, then dashed out. At least he could still run like normal.
Shadow turned out to be at home. If you could call it that. He'd taken up residence in a small flat that was as bleak and boring as he was.
Fitting that, Shadow was also being boring, just sat around watching the news.
Sonic realised he was on the news. Well, it was hardly surprising, people did know about him. It stood to reason that if anything happened to him, people would find out in short order.
"Hah. Wonder what he did to himself this time," Shadow mused. "Maybe he took a rock to the head and it's finally knocked the last of his sense out."
"Well, you're nice. It's not like you're any better, you don't even try to help people."
He leaned on the back of the chair, also watching the news.
"...and finally, it seems there's been an incident involving the notorious Doctor 'Eggman' Robotnic, leaving a number of jewellers missing across town. It's unknown what the motive is behind his most recent plan. With Sonic out of action, who knows what will happen next?"
"Oh, how bothersome," Shadow said sardonically. "Sonic's in a coma, so everyone's in a panic."
"So do something, lazy."
"I guess I could do something."
"That's freaky. It's like I'm making some kinda subconscious suggestion, and you're picking up on it." He had a sudden thought. Maybe if Shadow was picking up on what he was saying, he could persuade him to take action in his place.
"Why should I do it though... Tails or Knuckles will probably try and cover."
"Try and cover it, yeah, but maybe you should do something and make sure of it."
"No, can't leave it to them. They'd just mess it up. I'll have to do something instead."
"Heh. Good boy, Shadow. Go save the world for me."
Shadow got up and walked right past him, leaving Sonic with the annoying pull on him briefly.
Sonic decided to follow. What else could he do? He didn't exist, as far as the rest of the world was concerned, except in that hospital room. He doubted there was anything worthwhile to do there.
They both ran on out, heading toward the scene of the latest crime. The authorities were already there, but Shadow had no trouble gaining entry. Sonic hardly needed to worry.
Shadow poked around a bit. Nothing stolen, nothing missing – except the jeweller himself.
A note was left on the counter. A typically Eggman note, with a watermarked image of him smirking at them from behind the text.
The note essentially challenged anyone who dared to try to stop him.
"The guy must have tons of these things lying around," Shadow reasoned. "They seem to turn up exactly the same every time he comes up with some new plan."
"Duh. This is Eggman you're talking about. He never passes up a chance to taunt people like that."
"So he's after jewellers... but it looks like only the important ones. What could he be up to?"
"God you're slow. He's up to something with the Chaos Emeralds, no doubt."
"Or the Master Emerald," Shadow finished, as if he'd heard Sonic. He then seemed to realise he'd finished a sentence he hadn't started, and looked around. "Weird. I could have sworn I just heard Sonic."
"That's 'cause you did. You just don't know it yet."
Shadow shook his head, and left again.
"I wonder if Sonic's coma is related to this?"
"Naturally. I always stop Eggman, so he's always trying to get me out of the way."
"That's true... hey!" Shadow stopped, looking around again. "If you're haunting me or something Sonic, you better stop it."
"Why would I do a thing like that? This is fun." He stood in front of Shadow. "You know, you really oughta get out more. You look lost."
"I'm not lost!"
"Oh sure," he teased. "Never doubted it for a second."
"This is getting weird. I'm going to Angel Island... maybe I'll find something useful there."
Sonic forgot to stand out the way as Shadow ran through him. The pulling force he'd felt earlier was stronger, and as Shadow passed through him, he seemed to somehow catch on him.
Shadow slowed to a walk, looking puzzled, then just stopped.
Sonic was still overlapping him. He tried to move free, but found when he tried to move, Shadow did.
"Well, what d'ya know," he said in Shadow's voice. "I seem to have become you, Shadow."
"Sonic?" Shadow's voice sounded in his mind. "What've you done?"
"Me? I ain't done a thing. You ran right through me, and now it looks like I'm you." Sonic walked on for Shadow.
"Right through? What do you mean? You weren't there at all."
"I was, you just couldn't see me."
"So that was why I could hear you."
"Yup. That was me."
"What happened to you?"
"Some Eggman thing. It's stuck me in a coma, except somehow I'm also separate from my own body, and wandering around."
"So when I went through you..."
"I kinda borrowed yours, yeah."
"Get out."
"Would do, but I don't gotta clue how to, Shady."
"Shady?" Shadow's voice picked up an irate edge. "Shady!"
"Hey, easy. Getting all uptight over a nickname isn't gonna do any good."
"Shady..." he muttered angrily again. "Don't ever call me that again."
"Sure thing, Shady. I reckon we should go check out the Master Emerald."
"That's what I was going to do."
"I know, I heard ya say so, remember?"
"Go on then. It's not like I can do anything while you're stuck using my body, and I'm stuck just watching."
"Going already."
It took him a few moments to figure out how to run like Shadow. Shadow seemed to just skate along instead of run. It used less effort, if nothing else, but he preferred to run.
"Hey, Shadow?"
"What now?"
"Where'd you keep your Chaos Emerald?"
"None of your business."
"If ya think so. Gonna look a bit strange though, people seeing Shadow not using Chaos Control."
"You're not having it."
"It's not like I can steal it or anything."
"Not the point. I don't trust you."
"Someone got out of the wrong side of bed this morning."
"Shut up. Just keep running."
"What about you?"
"I'm going to see if I can figure out how to get you out of my body."
"Don't ya like the company?"
"Not if I have to put up with you."
"I'm not all that bad."
"Imagine if this happened to you, and you were the one trapped in your own body while I did whatever I wanted in it."
"You think I'd mind? I'm not as unsociable as you are."
"What about... if Amy were the one doing whatever she wanted instead then?"
That bothered him a little, but he hid it quickly. "Amy's been after me for long enough. She'd probably just use it to get closer to me. Sure you're not just worried about her doing to you what I am now?"
Shadow said nothing, but he could almost hear him seething at the thought.
Sonic brought his favourite grin to Shadow's face. It probably didn't look right, but it didn't matter. He could go save the world again, even if people were going to think Shadow had done it.