I tend to feel Sonic stories ought to have a 'version of reality' explanation attached to them, there's so many variations of canon. This one could fit almost anywhere as all the versions have some notion of Sonic and Knuckles meeting on the Floating Island when Robotnik tries to take the Master Emerald and in the process deceives Knuckles into believing Sonic to be the villain until All Becomes Clear at the end.
I've used one specific element from the Fleetway comic universe, namely the idea that during those events Robotnik discovered where Sonic's little band of freedom fighters were based. In the Fleetway version Sonic made their relocation to the Island a condition of giving Knuckles the Master Emerald back.
This story picks up a short while afterwards.
"How is he doing that?" Sonic stared up at Knuckles gliding back and forth above the craggy mountain face that marked the boundary with Lava Reef zone. "He's been up there hours. I thought the point about gliding was you had to come down eventually!"
Amy shrugged, shading her eyes with a hand to watch.
Tails said, "He called it 'ridge lift'. Something about the way the wind hits the hills. It works too. I tried it. You can even feel it in the Tornado if she's lightly loaded." He smiled "It was kind of fun."
Sonic waved dismissively, "Yeah, great if you want to stay in one place all day." He turned to head back to the makeshift village, then paused. "Hang on--you were chatting with Knuckles about this? When?"
Tails shrugged. "I don't remember. Last week sometime. The wind was from the other direction, it was over the other side of the zone, I was looking for somewhere sheltered to leave the Tornado in case it got blowier."
"And Knuckles just happened to turn up for a friendly chat?" Sonic looked sceptical.
"Um no, not exactly. He was--" Tails looked momentarily puzzled. "Picking flowers actually. Or had been. He had an armful. I didn't ask because I thought he was going to bawl me out for landing on the wrong bit of grass or something, but he just told me I'd be better off leaving the plane up this end of the zone. Last week's weather wasn't the prevailing wind apparently. So we got talking about flying, that's all."
Sonic forgot about the gliding to mentally back-pedal again. "He was picking flowers? Knuckles?"
"Uh, yeah. Those big yellow ones?"
"Oh those," Amy put in. " The seeds are edible. He dries them to store."
Sonic turned on her. "Oh so you had a nice friendly chat as well! Lovely! So why is it the only sentence longer than two words that I ever get from him is an insult?"
Amy laughed. "Oh, Sonic. Get that outraged look off your face. You know perfectly well you can't go more than three words tops, yourself, without making some smart-alec remark. Have you ever tried talking to him properly?"
Sonic stared at his two friends, completely confounded.
"He hates my guts, Amy. I'm the reason his precious Floating Island nearly ended up in the sea. As far as he's concerned I brought Robotnik here--I might as well have tried to steal the Master Emerald myself."
"That's ridiculous," Amy said.
"I'm sure he doesn't think that," Tails added. "You did work together to get it back."
Sonic dismissed that. "He'd have worked with biggest creep on Mobius to get that Emerald back. He did work with Robotnik, in case you've forgotten."
"You're being ridiculous again. If you're going to blame him for that, and he's going to blame you for crash landing here, then it's no wonder the pair of you are too stubborn to be civil to each other!"
"Who's stubborn!"
Tails gave a cough that sounded suspiciously like a laugh and Sonic flung his hands in the air. "Right! I'll go and pay him a neighbourly visit right now shall I? We'll see who can't be civil!"
Amy and Tails looked at each other.
"Oh dear," Tails said. "I hope there's not going to be another fight.
Knuckles had disappeared from the ridgeline by now and Sonic realised that he had no idea where the echidna normally spent his time. Of course this wasn't necessarily a problem for someone who could search a whole zone in a matter of minutes, and a faint spill of smoke into the evening air gave him a clue.
It turned out to be coming from Marble Garden, where Knuckles was fussing over an ashy fire. A large flat pan was full of what looked liked the seeds from the yellow flowers Amy had described. Several more of the plants were hanging upside down from a rail, with a cloth spread out beneath them.
"Hi," Sonic said.
Knuckles looked at him then went back to his fire and gave the pan a shake.
"Hello," Sonic said loudly. "So what're you up to?"
"Preserving food." Knuckles didn't lift his head from what he was doing.
Sonic looked around the verdant bushes full of fruit growing a few feet away, then back at Knuckles' hanging rail where strings of the same type were slowly wrinkling as they dried.
"You got something against fresh food?" he asked. "I thought the seasons didn't change here." He waved at the bushes. "This stuff grows all year round doesn't it?
"Usually." Knuckles turned. "What do you want?"
Sonic shrugged. "Just came to say hi."
Knuckles narrowed his eyes. "Very well, you've said it. Are you going to leave now?"
"Not very hospitable, Knux."
"I am not your host," the echidna said, flatly. "And that is not my name."
"Okay," Sonic plonked himself down on an overgrown piece of wall. "Sorry, Knuckles. Tails and Amy seem to think I'm missing some secret 'he's a friendly guy really' thing going on here, but apparently all I'm going to get is an armload of attitude. So d'you mind if I just hang around here long enough to convince them I made the effort so they'll stop nagging me?"
"Yes."
"What?"
"Yes. I do mind. I told you and yours to keep to Mushroom Hill."
"That didn't seem to bother you when it was Tails and Amy strolling around instead of me. So what's the problem here, Knuckles?" Sonic was frustrated now, and although he recognised the frustration for what it was it wasn't enough to stop him being angered by it. "I didn't bring them here because I thought it'd be a nice holiday resort you know! Maybe you think I did it just to rub your nose in the fact you needed my help to get your damn Emerald back?" He was back on his feet now, "I brought them here because it's my responsibility to keep them safe and this was the only place I could think of where I had the chance to do that."
"You're right. Knuckles said, coolly. "It is your responsibility. And that is why I am not interested in your friendship, and why I do not hold Tails' and Amy's and the rest of your people's presence against them. It is not their fault that you brought Robotnik down on them like you brought him down on me."
"You haven't got a clue!" Sonic snapped back, spluttering with indignation, not least because Knuckles couldn't know how painfully close to the truth that hit. "You've dealt with Robotnik for a week or so, I've been fighting him longer than I want to think about. And I've done it to protect people, Knux," he snarled out the diminutive and didn't care, "Not some pebble and a patch of ground. Real lives. So don't tell me anything about responsibility!"
He turned sharply away. Knuckles didn't follow when he broke into a run.
Sonic ran hard through the zones of the Island trying to burn off some of the infuriation. He didn't know why Knuckles had such a knack for getting his back up. Sonic was not used to being at a loss for a collected comeback and rarely let things get to him overmuch. Yet every conversation with Knuckles ended in a blazing row or an exchange of insults.
When he finally slowed and starting paying attention to where he was again, he found himself deep in Lava Reef, not far from where he had first found the entrance to the caves and the subterranean Hidden Palace with housed the Master Emerald.
Sonic wandered in that direction, keeping a wary eye out for the numerous traps and wards set around it. Then, for some reason he wouldn't have been able to name, Sonic continued on into the passageways, his aggravation slowly forgotten in the challenge of negotiating the hazards en route.
He stopped in the imposing hallway of the Palace, the room dominated by the picture covering an entire wall. Sonic stared at it, remembering his shock at his first sight of it. It was clearly meant to depict him, albeit in his Emerald-charged Supersonic form, along with his metal counterpart.
He touched the mosaic making up the picture. The colours were faded slightly, the stone and glass worn and dulled by time. It was clearly ancient. Yet the events it depicted had happened less than a month ago.
Sonic wasn't fond of mysteries and this Floating Island was full them. He no longer really distrusted Knuckles, but there were far too many questions the echidna was unwilling, or unable, to answer.
Sonic moved on. He climbed the long flight of stairs to the Master Emerald chamber and walked without stopping towards the gem. He stood in front of it, staring again.
The reason for his being here on the Island. The reason for Robotnik setting up base here. The reason, maybe, for Knuckles' weird isolation here.
Even standing a few feet away, Sonic could feel the power of it, rolling across the chamber like waves. The temptation to reach out to it, to take some of that power into himself was like an ache. A craving. A--
Sonic shook his head and turned away.
"Snap out of it," he told himself out loud. "Knuckles would have your hide on the wall along with your picture if he caught you here after today's happy little conversation."
He started towards the stairway when movement caught his eye, and he turned, and then froze, because there was Knuckles. Standing right there, on other side of the Emerald. His outline was distorted and discoloured by the view through the gem, but instantly recognisable.
Sonic opened his mouth to invent some explanation and stopped. Knuckles, incredibly, seemed utterly unaware of his presence.
Sonic stepped back towards the Emerald.
"Uh, Knux--" He winced. "I mean Knuckles--"
Sonic stopped short again because it was suddenly clear that the strange twist to Knuckles' body was no trick of refraction. He was limping, badly, and his left shoulder hung at an unnatural angle.
Sonic darted around to Knuckles' side of the Emerald, questioning as he went, "What happened? Was it Robotnik? How--" Sonic trailed off.
The chamber was empty.
He looked back at the Emerald. There was Knuckles, still apparently the other side of the Emerald from him.
"Knuckles?"
This time Sonic walked slowly right around the Emerald. No one.
He thought quickly. He'd only been here a few minutes and had arrived at near top speed. Knuckles had been still playing with his dinner when he left. He couldn't have got here in that time, much less had a fight on the way.
Sonic stared back at the echidna visible through the Emerald. It was Knuckles. Every detail.
The -- Illusion? Phantom? Whatever it was -- staggered. His left arm was carried tightly across his chest, hand tucked tight against his side by the opposite arm. He reached out with awkwardly with his free right hand to touch the Emerald and slipped to his knees. His fur was darkened in irregular patches. Sweat or blood, it was impossible to tell through the greenish tint. For a moment he lifted his head and seemed to be gazing directly into the Emerald. Directly at Sonic.
Sonic was unable to drag his eyes away. He knew it was an illusion of some sort. It was clear this other Knuckles couldn't actually see him, maybe wasn't even real at all. But for a second it had seemed as though he had looked him square in the eyes.
Sonic stepped back, shut his own eyes and shook his head.
"Weird place."
He looked back at the Emerald and would have been perfectly willing to believe he'd imagined the whole thing, as at first he thought the vision had disappeared. Then a flurry of something blew across the slice of room visible through the Emerald. Wind driven dust or something Sonic guessed. But the air in the chamber where he stood was perfectly calm.
He stepped closer. This time Knuckles was curled close to the base of the Emerald, almost out of view from where Sonic stood with his nose all but pressed against it.
What Sonic had take for dust was now clearly snow. It blew and drifted on the steps, swirled around the room in eddies and flurries. Knuckles appeared oblivious to it and didn't stir as it settled on his fur and melted on his face. His cheeks were sunken and his ribs protruded visibly from his matted fur. He looked more than half starved and Sonic felt something like horror as he recalled Knuckles' understated "usually" in answer to his question about the food and the seasons.
Was this the past he was seeing then?
The image changed again and Knuckles was sitting serene and apparently healthy on the edge of the top step. Again, and he was running towards the Emerald, flushed and breathless, eyes scanning the chamber for--what? Damage, or enemies maybe because the next flash was a snapshot of a fierce fight with several creatures Sonic didn't recognise.
He startled then as he recognised himself in the next image, Knuckles had his back to the Emerald this time, was facing that other Sonic. The one of a few weeks ago who had come here on the trail of Robotnik and found that he had more than one problem to contend with.
It was the past then. Some echo of the things the Emerald had seen. If "seen" was the right word. Could a gemstone have a memory?
"What are you doing here, hedgehog?"
Sonic whirled to face the stairs.
A very real and quite obviously very angry Knuckles stood in the doorway, fists clenched at his sides.
Sonic glanced back at the Emerald and Knuckles' tone changed, softened in a sort of understanding.
"Come away from it, Sonic. It won't show you anything new."
Sonic turned away with some effort and walked towards Knuckles. The real here-and-now Knuckles.
"I saw..."
"I don't--" Knuckles started angrily but again halted and moderated his tone, "I don't want to know what you saw. It is none of my affair." He did lose his grip on his voice for a moment as he finished, "In truth it was none of yours either!"
Sonic was silent a moment, then had to ask, "Are they real? The things it shows?"
"Yes."
Knuckles headed down the long flight of steps and, too bewildered by what he'd seen to think of doing otherwise, Sonic followed.
Knuckles led him outside without further comment. He turned as soon as they reached daylight and headed back up into the hills.
Sonic stood outside the passageway entrance, watching for a moment. It wasn't usual for him to be lost for words, but he felt uncomfortable with what he'd seen, as if he'd been caught eavesdropping or spying.
After a few moments he shook himself and ran in the opposite direction to that Knuckles had taken, back to the valley at the base of Mushroom hill where Amy and Tails were still chatting.
Amy spotted him first.
"So, did you find Knuckles?"
Sonic nodded slowly.
"And?"
Sonic shrugged. "We talked a bit."
Tails looked at Amy who looked at Sonic appraisingly.
"Alright -- we argued," Sonic admitted. "Like I said, he thinks the whole business with Robotnik is my fault."
He stopped, hesitant to tell the about the Emerald.
"I don't--" he paused, but his curiosity was too great "I don't suppose he mentioned to either of you how long he's been here on the Island did he?"
Tails and Amy both shrugged, puzzled by the sudden change of direction.
"Never mind," Sonic said, flicking his fingers. "Just a thought. Anyway you can't say I didn't try."