Author's Notes:

Well, it's been a while since I updated this one. It took me a little while to sort things out.
I was going to leave a note here, but it'd spoil stuff - so it's at the end instead.
Read on.

Shadow grumbled and squirmed while Amy worked the colouring into his fur, Sonic trying not to laugh too loudly at his somewhat unlucky crush.
Aside from Shadow's distinctive quills and footwear, he was starting to resemble Sonic. This, Amy had told them, was a key part of the plan.
Shadow's fur was almost as stubborn as he was, it's black colouration refusing to give in to the blue easily, requiring more work or ink in some places than others. The red gave in easily, so after his legs had put up stiff resistance, she'd started there, causing him to complain about getting it in his eyes.
Amy just told him to stop being such a baby, continuing.
Tails, meanwhile, was off seeing to Sonic's own body at the hospital. He wanted to bring it to his own workshop, using the excuse that he had a cure, and they didn't. It had worked, they'd been told, but were still waiting for him to get back.
After a brief argument, Shadow has persuaded Sonic to find Knuckles. They hadn't told him about what they'd planned except to capture one SWATbot, complete with the still as-yet unidentified extras. Tails had stubbornly refused to explain their purpose to any of them.
Knuckles, sprawled in one chair, was watching the proceedings with a wide grin, which only made Shadow grumble more.
"You know, you don't actually look all that bad, Shadow," Knuckles told him. By now, he was almost completely blue. He looked like Sonic having a bad day.
"I'd like to see you go through this," he retorted sharply.
"Me? I'm not a hedgehog," he grinned back. "I wouldn't do a good Sonic impression."
"Exactly, you got it easy."
"Oh, stop complaining," Amy interrupted. "You're done. You'll have to borrow Sonic's shoes, your own ones would give you away."
"The quills," he said, not trusting himself to say anything else. Amy considered him a moment, then told him to stay there, and ran off looking for something. "Now what is she up to?" he mumbled.
The door knocked. Shadow glared at Knuckles. He wasn't going out like this just yet.
"Oh, alright. Just because you don't want to show off."
A few moments later, Sonic watched uncomfortably as his own body was brought through by Knuckles and Tails. He still had trouble coming to terms with seeing himself.
They paused to let Shadow steal Sonic's shoes, then continued on to wherever Tails wanted to put him.
"Your shoes are a little loose," he told Sonic.
"You're just too used to your own, they're a bit tight."
"Don't want them to come flying off."
"You don't need to worry about that now."
"You're doing the running."
"Never doubted it for a moment. Think you're up to being me?"
"I might just leave it to you."
"Fun – I get to take over for you again."
"You're enjoying this, aren't you?"
"Can you blame me?"
Shadow almost replied, but Amy returned with several combs and various other things, ordering him to sit down so she could work on his quills.
"The things I do for you lot," he grumbled, but there was a faint smile playing on his face as he glanced at where Sonic was.

Oh, how more perfect could you get? The Echidna had left by his own accord, saving Robotnik the effort of having to come up with a plan. It took only a few moments to switch the Master Emerald for his fake, and leave again. No one would ever suspect a thing.
The console in front of him beeped.
"What is it?" he barked at it, answering the call.
"Attack detected," a computerized voice responded.
"Who by?"
"One hedgehog. Blue. Identified as Sonic."
The console did not respond. He'd stopped it from answering back.
Instead, he just opened full throttle, getting back the base quickly. The sooner he got to the root of this the better. Sonic was meant to be in a coma for as long as he wanted. And not only that, whenever he wanted, if his theory held true. He'd never have to worry about the hedgehog again.
So what was going on?
Sonic was, in fact, enjoying himself as usual, causing generalized chaos the way only he could. Shadow had relented, and had shown Sonic how to borrow his own Chaos abilities. If anything, they made it even more fun for him.
"Keep an eye out for those SWATbots," Shadow told him.
"Yeah, yeah, I haven't forgotten. They'll be around soon, no doubt."
"How can you be sure?"
"Simple. Old Eggy thinks I'm in a coma still, right?"
"Amy made you look like me, right?"
"Yeah..." he was beginning to understand the idea already.
"So, Eggy thinks you're me. And with my look and personality, anyone who didn't know would think it really was me."
"I get it. He'll have to look, and once he realises it's you again, he'll send another one to do the same thing the first did, to make sure of it."
"Right, and when that happens, we lead it into Amy's trap."
"Amy makes good plans."
"Hey, I made some suggestions too," he objected.
"Yeah, and she rejected them, remember?"
"I'm an integral part of the plan, you could never pretend to be me accurately."
"Oh yeah?" Shadow would have grinned if he could. "I run real fast, have a crazy hedgehog girl chasin' after me, and I got a secret crush on Shadow." It had been an almost perfect impression.
"Stop that!"
"Look to yourself, just ahead."
"Gottem," he grinned, landing on a robot and kicking a few parts off before jumping off again.

It was unmistakably him! This was impossible, but here he was, wreaking havoc as some kind of revenge or something.
His robots weren't doing any good, they never did against Sonic.
A moments hesitation, then he punched out the order to send in the experimental SWATbots again. They'd worked the first time. There was nothing to stop them working again. He'd have to do something to stop the rampaging hedgehog... before he found out about the Master Emerald.

"You get any more close calls like that, and I'm going to be feeling it for weeks."
"Oh, relax, Shady. I never get hit, I'm too quick."
"I'm not as quick, remember?"
"Why d'ya think I'm using your Chaos control as well?"
"Eh, guess you got a point there. Just... watch your back. Or mine."
"No trouble after this."
"Look there. One SWATbot, complete with the weird stuff."
"Looks like Amy was right."
"And me."
"Yeah, only because you remembered the plan."
"You're taking all the fun out of this, Shadow."
"Stop complaining. I don't want to be in the same position you're in."
"Nah, that's up to Amy and me."
"Don't you mean Sonic and you?"
"Not yet, Shady."
The lumbering SWATbot plodded after them, paying no heed to anything around it, kicking remains of other robots aside and occasionally whacking it's head on a low beam or pipe. It didn't seem to care. Of course, almost all of Robotnik's robots weren't even programmed to care, they were just there for Sonic and friends to break, he always thought.
The steady supply of other robots finally petered out, leaving just the SWATbot following. It was lead down several corridors, most of which still intact but for a few marks of Sonic's explosive entry – courtesy of Tails and a hand from Shadow's Chaos Emerald.
They emerged at the same Colosseum where he'd first met these SWATbots, kicking up a stream of dust behind him. Amy was watching for it, signalling to Knuckles and Tails. As the bot wandered in, they both tugged on a previously well hidden rope, and tripped it up. Amy in turn cut several ropes above where it fell, dropping a cage on it, which finally triggered a pressure plate underneath, adding another line of bars underneath, allowing for easy transport. It tried to stand up, but was forced to stop, having no room to move.
"Neat," Shadow commented. "I knew she'd make a better Sonic than you."
"You're not gonna let me forget that, are you?"
"And miss all the fun of teasing you with it? Of course not."
"Fun, Shadow? You? I'm amazed."
"You just don't know me well. Yet."
"Yet," he agreed, remembering what the two of them intended to do.

It wasn't well known that Tails had a streak of medical knowledge in him, so it was a bit of a surprise to find that hidden somewhere in his workshop was a room that looked for all the world like someone had taken a piece of a hospital, and slotted it in.
He was wandering around, checking displays, tweaking machines, doing... whatever it was doctors always seemed to be doing. Sonic lay on one cot, completely unaware of his mind being off with Shadow. A blank look and shallow breathing were all that showed him still to be alive, but even they were hard to tell among the various wires and pads attached to him and the equipment
The other cot was similar to the one Sonic was laid out on, except there was no one laying on it just yet.
A crash from downstairs indicated the SWATbot was still stupidly trying to break loose while Amy tried to get close safely. It was the only part of her plan she'd been afraid of.
"Nervous?" he asked the empty air.
"How did you know I was there?" Sonic's voice replied.
"Just a hunch."
"A bit nervous. Amy is too though, so all's fair."
"You're going to have to adjust you know."
"So's she. We can help each other out."
"Won't Shadow object to that?"
"What for?"
"Assume for a moment Amy was your girlfriend, and she was hanging around another guy."
"Gotcha, but I don't think like that. Wouldn't feel right to me anyway."
"If you're sure."
Sonic didn't reply, mostly because Knuckles and Shadow were carrying Amy through the doors. She was in the same condition Sonic was currently in.
Knuckles, uneasy, helped get her onto the remaining cot, then left. He still didn't know the full idea, and he didn't look like he wanted to. Besides, he had an Emerald to guard.
It was Shadow's turn to look uneasy now, watching the two of them, wondering if it would work.
Tails checked the displays, attaching similar wires and pads to Amy, checking one last time, then gave a critical nod, and stepped clear, which was the prearranged signal to each of them that everything was ready.
Sonic's monitors began to show differences first, indicating increased brain activity usually associated with someone rousing themselves from a deep, long sleep. Amy's followed close behind, but neither woke up just yet.
Shadow shifted from foot to foot uneasily. He'd taken back his own rocket shoes, returning Sonic's, and his quills were starting to return to their usual positions, but he was still blue in colour.
"Shouldn't they have-" he began.
"Not yet. It takes a few moments. Amy will likely wake first."
"Which Amy."
"Your Amy," Tails replied with a faint grin.
He wasn't wrong. She woke up, yawned, blinked a few times, then looked around, flashing Shadow a smile. He went to her side just as Sonic awoke. He sat up, also yawning, then looked himself over. Apparently satisfied, he glanced to one side and grinned at the sight of Shadow and Amy. It looked like everything had gone perfectly to plan.

Author's Other Note:

Yeah, told you I was putting it here, didn't I? As you might of gathered, as of that last paragraph, you can assume they've taken on each other, and for simplicity's sake, they'll use their new names instead.