Archive of Our Own ^beta

Chapter Text

Knuckles dragged a gloved hand down his face, exhaling slowly as the glow from the desk lamp painted harsh lines across his features. Shadows bled into the corners of the room, thick and unmoving, while the ticking of an old wall clock echoed like a drumbeat in his skull. Beyond the thin walls, muffled voices carried—busy chatter, strained orders, someone yelling about a broken generator—but inside, the war felt quiet.

He stared at the stack of papers in front of him like it might bite. Logistics, supply chains, med reports, mission briefs—it was all there. A hundred decisions waiting to be made, and every single one of them could mean life or death.

What the hell did he know about leading an army?

Training exercises, sure. Sparring sessions? Absolutely. He’d stepped in plenty of times to bark orders, teach discipline, push the others past their limits. But that was controlled. That was safe. That was nothing like this.

The Resistance wasn’t a team—it was a war machine held together with duct tape and desperation. Soldiers, medics, scouts, engineers, pilots, civilians trying to play soldier... and Knuckles was the one at the wheel. One bad call, and the whole thing would come crashing down. And when it did? That blood would be on his hands.

His grip on the pen tightened, and the tip tore into the corner of the paper beneath it.

Then there was Sonic. The thought was like a punch to the gut. Knuckles clenched his jaw, breathing through his nose.

He should’ve been here. Sonic should’ve been the one leading them—rallying troops with that reckless grin, diving headfirst into danger like he always did, somehow always making it out in one piece.

But he wasn’t here. He was gone—captured. And Knuckles had to pretend that it didn’t kill him every second of every day.

They were more than friends. More than partners in the battlefield sense. Mates. That word meant something to Knuckles. It wasn’t just a label—it was a bond, raw and real and impossible to sever. Even now, even through the crushing pressure of command and the slow bleed of hope, he could feel Sonic’s absence like a hole in his chest.

The world didn’t stop for grief. Especially not after Infinite’s attack. That bastard had come out of nowhere, tearing through their defenses like wet paper. The Resistance had barely survived. Too many wounded. Too many scared. Morale had shattered like glass.

And when no one else knew what to do—when even the veterans were frozen in fear—Knuckles had stepped up. Someone in the right mind had to.

Amy had been too busy saving lives to think strategy. Tails... Knuckles didn’t even want to talk about the state the kid was in. Silent. Broken. A ghost of himself. Silver tried, really tried, but he was shaken too—flickering between hope and despair like he couldn’t decide which one to hold onto. Rouge? She was running her own game, useful, sure—but she wasn’t stepping into the spotlight.

So Knuckles had done it. Not because he wanted to. Because no one else could. They needed strength. Certainty. He had always been that. Or at least, he could pretend long enough to make it true.

But late at night, when the world went quiet and the weight settled in his bones, the question came back like a bad dream.

"Why did you leave Angel Island?"

People assumed it was the Master Emerald—that maybe Eggman had made a move, that Knuckles had come down to protect it. Logical. Sensible. Wrong.

The truth? The Emerald was never in danger. Not from the outside. It was gone because he had taken it. No. Not taken. Absorbed.

Knuckles’ eyes flicked toward the ceiling, like he could see through the concrete and steel and reach up into the clouds. But there was nothing there now. Angel Island had fallen—slammed into the sea like a forgotten relic. Because without the Emerald, it had no anchor. And the Emerald? It wasn’t on the island anymore. It lived inside him.

When he'd fused with it, everything changed. He felt it now—its hum in his bones, its power threading through his veins like wildfire. The cost? Everything he had once known. His home. His legacy. Maybe even his soul.

But he didn’t regret it. Not really. The war needed power, and he'd given it everything he had. Still, the thought made his throat tighten. That sacrifice didn’t make him special. It made him accountable.

He shook himself and turned the next page. Medical shortages. Troops too injured to return to the field. A request from the scout unit—two had gone missing. Maybe captured. Maybe worse. Stupid, useless paperwork. Every line of ink a cry for help.

He wanted to burn it. He wanted to throw the desk across the room, punch a hole through the wall, scream until his voice was gone. But he didn’t. He couldn’t. He just kept reading.

The names on the list blurred together. So many people—Mobians, humans. Some barely old enough to be in this fight. All of them looking to him for answers. For direction.

And sometimes, Knuckles wondered if they looked at him not because they trusted him… but because they had to.

Maybe they sensed it—that deep down, he didn’t belong here. That the one who should be leading them was trapped in a cell, enduring gods knew what at Eggman’s hands and they were stuck with him instead.

A sharp knock cut through the silence.

"Knuckles, meeting." Silver’s voice, quiet but steady. At least he was trying.

Knuckles closed his eyes for a second, then pushed himself up. The chair creaked under his weight as he stood, careful not to knock over the piles of paper stacked around him. His hands weren’t built for this kind of work. They were made for smashing, for protecting, not for paperwork and command briefings. Yet,  here he was.

He cast one last glance at the mess on his desk before turning toward the door. The hallway outside was dim, lit by flickering lights and hope running on fumes.

He didn’t know if he was the leader the Resistance deserved but he was the one they had. Until the day Sonic came back—if he ever did—Knuckles would make damn sure the fight didn’t stop.

Knuckles took his seat at the head of the table, the heavy chair sliding forward as one of the younger assistants, a fox mobian he hadn’t learned the name of yet, gave it a gentle push from behind.

"Here you go, Commander," she said softly, placing a glass of water at his side before laying out a neat spread of folders in front of him—scouting reports, movement logs, casualty updates, a few maps, and, oddly enough, a hand-drawn note from one of the children in the underground bunker: a crude sketch of him with big fists and a smiley face. He blinked at it but said nothing.

He didn’t ask for the extra attention. Didn’t need it, either. But the girl kept showing up at every meeting, quiet and precise, always making sure he had everything he might want before he asked. He wondered, vaguely, if she was afraid of him. He hoped not.

He didn’t bite. The echidna offered her a nod, that was all he gave. She nodded back and hurried to the door without a word.

Around the table, the others were gathering. The room was dim, as always, the only real light coming from the projector in the center and the wall monitors flickering with static maps. Despite the exhaustion that clung to them all like smoke, Knuckles could tell they were trying—trying to hold themselves together, to look sharp, to feel like leaders.

Rouge stood with her arms crossed, already skimming through a folder with that ever-present calculating expression on her face. She looked flawless, as always, though Knuckles could see the strain in the way she held her jaw. Silver leaned over her shoulder, lips pressed into a tight line as he absorbed whatever information she was feeding him.

Vector sat back in his chair, arms folded behind his head, chewing gum like the meeting bored him to death. Espio, calm and collected as ever, stood by the wall, his eyes scanning the room like a silent sentinel.

Charmy, Amy, and Tails were absent. Knuckles didn’t ask why. He had a feeling he knew. Amy had been spending most of her time with the injured lately, and Charmy... well, ever since the last mission went south, Charmy had barely spoken. Tails? He hadn’t been seen much at all, for good reasons.

The door clicked shut, and Knuckles straightened.

"Let’s get started then."

The meeting went on for over an hour.

They spoke in turns—strategies, defensive positions, patrol routes, enemy movements. Rouge had gathered intel from her informants: Eggman’s forces were shifting west, consolidating troops around the old supply tunnels. Silver offered to scout ahead using his powers, though Knuckles waved it off for now—he didn’t want to risk losing him too.

Espio spoke up about some minor sabotage success in one of Eggman's outposts—explosives planted, machinery wrecked. They’d bought some time.

Vector grunted, "we’re holding up, but barely. Our supply lines are trash. Half the troops are runnin’ on caffeine and adrenaline."

Knuckles nodded. "We’ll need to start rotating units more carefully. No one should be out there more than they have to. Get me those reports by tonight."

"I already have them," Rouge said, sliding a folder across the table, "I highlighted the critical teams."

Of course she did. Knuckles gave her a nod of thanks.

Then it hit. A surge of energy ripped through his chest like lightning.

His spine locked up. His breath caught. For a second, he swore the entire room dimmed, a low hum vibrating through his bones. The Master Emerald’s pulse—deep, ancient, undeniable. It was familiar now. Regular. But no less jarring. His fists clenched under the table.

"Commander?" A voice, distant and muffled.

He blinked, "What?"

Silver leaned forward, "I said, should we move Team Delta to Sector Seven, or do you want them to hold their ground at the riverbase?"

Knuckles exhaled slowly, trying to ignore the burning pulse still echoing in his ribs. "Hold them where they are for now. We’ll reassign them when we get word from the east recon team."

Silver gave a nod, but his brow furrowed. He didn’t believe Knuckles was alright. The echidna could tell. He didn’t care.

"Alright, we’ll wrap it up here," Knuckles said suddenly, his voice low but firm, "I’ll review the rest on my own tonight."

Rouge arched a brow, "you sure?"

"Yes."

He stood, "dismissed."

No one argued.

As the others filed out, murmuring quietly among themselves, Knuckles felt the tension drain from the room—but not from himself. The energy from the Emerald still vibrated beneath his skin, like a whisper he couldn’t quite hear.

He walked the quiet halls back to his quarters, ignoring the salutes from the guards as he passed. The base always felt too sterile. Cold. It was functional, secure... and completely foreign to him.

His room wasn’t much better. It was large, by most standards. Spacious, with a decent view of the mountains outside. There were a few personal touches—a couple of framed mission photos, a shelf with old relics Rouge had found, and the crude bed pushed against the far wall.

He stared at it for a moment. The bed, the thing that had baffled him when he first arrived. He hadn’t even known what it was.

Back on Angel Island, sleep wasn’t a luxury. It was a weakness. When he did sleep, it was sitting upright against the shrine, or sprawled out on the stone, waking hours later with a stiff neck and numb legs. There had never been comfort. Never been softness.

Someone—Amy, probably—had explained it to him, what a mattress was and why it was important. It had been weird, at first. Now he kind of liked it.

Knuckles sat on the edge, his massive shoulders slumping slightly. He pulled off his gloves, flexing his red scarred hands. The pulse was still there, still humming, it was still watching.

The Master Emerald used to speak to him. Not in words—but in feelings, images, emotions that passed through him like wind through trees. On Angel Island, he’d felt it constantly, like a heartbeat against his soul. It had told him things. It warned him and guided him in the right direction. Now? There was only silence except for those energy waves.

"What do you want?" he muttered aloud, staring at his hands, "why won’t you say anything anymore?"

Nothing. Not even a flicker.

"I'm trying to do what’s right. I’m doing everything I can. So what else do you want from me?"

Still nothing. He didn’t know whether to be angry or just tired.

His fists relaxed slowly, and he laid back on the bed, staring at the ceiling. The hum of the Emerald's power settled into the background of his senses, dull and familiar. Like an ache he’d stopped noticing.

Eventually, his eyes drifted shut. For a moment, just a moment, he thought he heard something. Not a voice. Not words. Just... the sound of wind, waves and distant thunder.

The harsh flick of a switch overhead sent a flood of cold, sterile light across the room. Sonic winced, blinking against the sudden brightness as it stabbed into his skull like needles. He turned his head slightly, trying to pull away, even though the chains around his wrists clinked tight and unmoving.

Eggman’s boots echoed as he stepped into the room, his hands behind his back, that smug grin plastered across his face.

"Well, well," the doctor drawled, his voice too loud, too cheerful. "Hope I didn’t wake you, rodent or were you dreaming of better days?"

Sonic didn’t answer at first. His head lolled slightly against the wall behind him, chest rising and falling slowly. His arms were suspended above him, locked into reinforced clamps—too thick to break, even for him. The shackles around his ankles were connected to the floor. His legs trembled occasionally from the effort of standing upright all day. He wasn’t broken. Just... tired.

Still, his lips twitched into a crooked grin, "Eggman... you ever think about getting a hobby that isn’t me?"

Eggman gave a dramatic sigh, "why would I? You’re so entertaining."

He stepped forward, glancing at the display monitor nearby before turning back to Sonic with an almost-too-casual shrug, "and speaking of entertaining... I thought it was time we had a little chat. About your dear, mysterious boyfriend."

Sonic stiffened—just slightly. Barely noticeable to anyone else. Eggman saw it.

"Oh, don’t look at me like that," Eggman said, circling the room slowly, "you think I don’t know? I always suspected you and that echidna were close. But the bond—oh, no. That I didn’t realize until recently. Fascinating, really. A life-mate bond. You disgusting little creatures are always full of surprises."

"Don’t talk about him," Sonic said quietly, bitterness in his voice.

The round doctor only chuckled, "you should’ve told me sooner. I’d have used it against you ages ago. But, lucky me, I still got to stumble across something very interesting. You see... I had Angel Island surveyed after it came crashing down. Quite the tragedy, wasn’t it?"

Sonic’s heart began to pound, confusion settling over his body, "you’re lying." He had to be.

"Oh, I wish I were," Eggman said, now inches from him, eyes gleaming, "but there was nothing left up there. No emerald. No Knuckles. No shrine. Just ruins. Abandoned. Dead."

Sonic’s chest seized, "you found him, you're lying to me," he snapped. "You couldn’t have seen—he’s not—"

"Oh, I looked," Eggman interrupted smoothly. "I scoured the wreckage. No signs of life. No trace of the Master Emerald either. Which makes things very curious, wouldn’t you say? Where is it? And where is he?"

Sonic yanked at his chains with a sharp metallic clank. "He’s alive," he growled, "i’d know if he wasn’t."

Eggman leaned in, "would you?"

The words hit harder than they should have. Sonic’s breath caught.

"We both know what happens when a bonded mate dies," Eggman said, his voice lower now, colder, "the pain. The unraveling. The collapse. So tell me, Sonic... how are you feeling these days?"

That was it. That was the strike.

Sonic gritted his teeth hard, "you shut up."

"Your powers are sluggish. You haven’t made a single escape attempt in days. And I’m told you’re not even eating properly anymore.” Eggman tilted his head, "doesn’t sound like a hedgehog with hope to me."

Sonic’s fists trembled, "I said shut up."

"Maybe he’s gone. Maybe you’re all alone now," Eggman leaned close and in a whisper, "maybe you failed him."

"SHUT UP!" Sonic screamed. The room echoed with the cry, raw and broken.

Sonic’s knees gave out, slamming into the floor with a painful crack as the chains kept his arms suspended. His head dropped forward, shoulders shaking. His breath hitched—then came the tears. Hot, fast, angry. He couldn’t stop them. Not this time.

"He promised—" Sonic whispered, barely audible, "he promised we’d find each other again if we ever got seperated..."

Eggman stared in silence. Then, like some twisted conductor, he simply straightened his coat and turned to the monitor, "oh, don’t worry. I’m sure he tried, but we all know trying doesn’t always mean succeeding."

Before Sonic could curse at him again, a sharp beep erupted from the control console.

Eggman’s brows furrowed, "what now?"

The screen flickered, then shifted. Metal Sonic’s sharp-edged voice buzzed through the speakers.

"Intrusion. Low-frequency chaos anomaly detected near southern resistance stronghold."

Eggman’s head tilted, "chaos anomaly? Define."

"Unknown. No registered emerald signatures within resistance. However," Metal paused. "Energy levels surpass recorded chaos emerald output. Similar structure, higher magnitude."

Sonic’s head jerked up.

"What?" Eggman muttered. A new alert flared across the screen.

[SYSTEM NOTICE: ALL EMERALD-BASED POWER SOURCES DEPLETED. ENERGY SIGNATURE LOST.]

"What in the hell—?" Eggman whipped around just as the entire room shuddered.

A wave of blinding white-green chaos energy pulsed outward through the walls like a thunderclap. Lights shattered. Screens shorted. Every machine powered by chaos energy across the base died.

Alarms wailed, only to stutter and cut out entirely. The lab went dark. Only the emergency red glow remained, pulsing faintly like a heartbeat.

"Report!" Eggman barked, "What just happened?!"

A scrambling robot burst into the room, smoke trailing behind it, "Doctor! All systems tied to chaos energy have shut down! The emeralds, they've lost all power! They're inert!"

Eggman turned slowly, "What?"

"They’re just rocks now, sir."

Sonic didn’t speak. He sat there, hunched over in the dim red light, tears still staining his cheeks.

But his eyes were empty now. Completely empty. He wasn’t even confused. He didn’t care what that power surge had been. Didn’t care what Eggman lost or found or feared.

Knuckles was gone. His mate was dead.

To Sonic... that light could’ve been heaven or hell and it wouldn’t have mattered because it wasn’t him, it wasn’t Knuckles.

The moment the energy wave tore through the resistance base, everything went to hell.

Knuckles had been back in his quarters, hunched over the dossier Rouge had slid to him earlier—some kind of army team summary she wanted him to "seriously consider." His eyes scanned the lines, but his mind wasn’t really in it. His body ached. His soul felt like it was dragging iron chains behind it. Then the chaos wave struck and it wasn’t t all subtle.

It slammed into his chest like a meteor, searing through every nerve, rushing through his bloodstream like wildfire. The room blurred. His vision went white. His breath hitched. The echidna staggered to his feet, one hand bracing against the edge of the desk.

A low rumble vibrated through the walls.

The glow hit his eyes—green, bright and violent, flashing in a split second before dying down again. No one saw. No one could see as he was locked up in his room.

Inside, the Master Emerald screamed.

His chest heaved, claws digging into the desk's edge hard enough to crack the wood. Then, slowly, as the energy calmed, he straightened, dragging a hand down his face.

"...What the hell was that?" He whispers under his breath, confusion overtaking his body. It felt so familiar, chaos energy but that didn't make any sort of sense.

Red emergency lights began to flare outside. Sirens wailed. Doors beeped and failed. The sound of panicked voices rose in the hall. Systems were shorting. The base was in chaos. Knuckles stepped out.

The corridor was dim, bathed in crimson flashes. Resistance members—Mobians and humans alike—scrambled to figure out what had happened. Shouts echoed. Panels sparked. The smell of burnt wires filled the air.

"Something overloaded the core system!"

"All com-lines are down! External power’s failing!"

"What was that energy wave?!"

Knuckles didn’t say a word as he pushed through the corridor. His boots thudded heavily against the metal floor, every step making his pulse throb harder. He reached the central lobby—a wide circular space lined with monitors that now displayed static or flickered helplessly.

People turned toward him. They always did.

He ignored their eyes. He didn't have answers at the moment, he himself didn't know what it was. He did have an idea though, but there wasn't enough evidence to prove so.

Rouge found him almost immediately, "Knuckles!"

He turned, "what the hell’s going on?"

"I was gonna ask you that," she said, stepping close, wings drawn in tight. "That pulse—none of our sensors picked it up until it was already here. It hit every system across the base. It wasn’t electrical... it was chaos. I’ve seen what emerald energy does to circuits. This was different."

Knuckles’ jaw tensed and he decides to state what he thinks, "maybe it was a flare. The Chaos Emeralds can do that if they’re overcharged."

Rouge narrowed her eyes, "and you just know that?"

"Rouge, now’s not the time—" he tries.

"No," she snapped, cutting him off. "Don’t pull that. Don’t deflect. You’ve been acting weird for weeks. You’ve been distant, cagey, snapping more than usual—hell, even Silver noticed. You think I can’t tell something’s off?"

Knuckles clenched his fists as Rouge folded her arms, "you’re lying to me right now. Again."

"I’m not," he lied, and it came out too quickly.

She glared at him, "Don’t insult me."

He looked away.

Rouge took a step closer, lowering her voice. "You know something. You felt something when that wave hit. Didn’t you? I know how connected you are with all the emeralds."

"I said I’m fine." That familiar hothead was rising and he was trying to force it backwards. The emerald fed on emotion, he didn't need it to lash out.

She exhaled through her nose, eyes narrowing, "okay. Then maybe this will jog your memory. What happened to the Master Emerald?"

His head snapped toward her, eyes wide for a second before he caught himself, "I—what?"

"I went up there," she said, voice tight, "to the island. Figured maybe some jewel hunting would help me clear my head. The island’s gone, it’s fallen, just rubble and ruins and your shrine buried under vines. The Master Emerald is gone. So don’t you dare lie to me again, Knuckles."

People nearby were beginning to glance their way. Knuckles' hands shook.

Rouge’s voice dropped low, furious: "You did something and I don’t know what, but I know you. I know that whatever happened to Angel Island—it wasn’t natural. It wasn’t an attack. You took the Emerald and you did something and now you’re sitting here pretending like none of it happened, like everything's fine."

"Back. Off," Knuckles growled, tiny vampire-like fangs baring just slightly. They could hurt somebody bad if they wanted despite their size.

"No! You don’t get to shut down now! You don’t get to lie to all of us when we’re already on the edge of collapse! You owe us more than that!"

"You think I wanted this?!" he snapped, finally turning fully toward her, voice echoing through the lobby, "you think I asked for this kind of power? For this kind of responsibility?! I had no choice, Rouge!"

Rouge blinked, startled—not at his anger, but at the energy. His fists were glowing faintly now, barely visible in the red flashing light, but unmistakable. She didn't know but the Master Emerald was reacting inside him again—flaring under stress, reacting to emotion like a wildfire to dry air.

Knuckles froze. He hadn’t even realized it was happening. He forced himself still and then turned away sharply, heart pounding, "don’t ask me again."

"Knuckles, you’re—"

"I said drop it, I have too much to deal with at the moment," he stormed off, boots slamming the floor.

Rouge watched him go, jaw clenched. That energy—that wasn’t from any Chaos Emerald she’d ever seen. That was something deeper. Older. Stronger and whatever it was...Knuckles was losing control of it.

The red glow of emergency lights had finally faded, replaced with the steady hum of normalcy. Systems flickered back online, screens rebooted, and the alarm klaxons went mercifully silent. People began moving with direction again, the tension still thick—but now manageable. Controlled.

Rouge stood in the middle of it all with her arms crossed and her thoughts heavier than ever.

She exhaled slowly, then turned and made her way down the corridor, boots clicking softly against the metal floors as she passed the medbay and makeshift barracks. She stopped outside Tails’ door, knocked lightly once, and pushed it open.

Amy sat beside the young fox on the edge of a cot, gently rubbing his back as he stared listlessly at a cluster of open screens filled with raw data streams. His tails lay limp behind him, his ears flat.

"You guys missed a meeting," Rouge said quietly, not unkindly.

Amy glanced back over her shoulder, giving Rouge a tired smile that didn’t quite reach her eyes, "yeah... figured. Sorry. Tails wasn’t in the best place to be around people."

Tails didn’t even look up, "what’s the point in talking about troop formations or recon sweeps when we don’t even know what we’re fighting anymore...?"

Rouge’s expression softened, "I get it. Believe me. But something big happened after that meeting."

Tails blinked slowly, as if dragging his attention back to the present, "the energy wave."

"Exactly."

"I’m already running diagnostics," he muttered, gesturing to the flickering monitors, "it was chaos-based. That much is certain. The energy signature matches the Chaos Emeralds’ frequency… but something’s "wrong."

Amy frowned, "wrong how?"

Tails leaned forward, tapping a few keys. The screen zoomed in on a waveform diagram, erratic pulses displayed in chaotic patterns.

"See this?" he said, eyes scanning the data, "these are the base frequencies of the Chaos Emeralds. Every time they’re used, even when Eggman’s machines draw from them, there’s a traceable echo. But whatever hit us today… it was like the emeralds were disabled. Just—cut off. Deactivated."

Rouge stepped forward, eyes narrowing, "wait, what do you mean deactivated? That’s not possible."

Tails shook his head, "it shouldn’t be. Nothing short of a complete power drain or a direct override could do something like this. But these readings... they show the emeralds going dark. Every. Single. One."

Amy's breath caught, "but Eggman has them. He’s using them. That’s how he’s keeping Sonic—" she stopped, swallowing.

Rouge’s arms slowly crossed again, mind racing, "then either Eggman’s machines overloaded—"

"No," Tails cut in, finally turning toward her, "it wasn’t from his side. It came from ours. The wave originated here—from inside the base.”

That hit both women hard.

Rouge’s brow furrowed, "that’s not possible. We don’t have any emeralds here. We’ve been tracking all known Chaos signatures since day one. The last confirmed one was weeks ago, and all of them are still with Eggman. That wave came from his base to over here and i’ve personally scanned every supply drop and tech cache that’s come through this place."

Amy’s voice was quiet, "then how…?"

Rouge didn’t answer right away. Her mind drifted—back to Knuckles. Back to the flash of green in his eyes, the faint glow in his fists when he snapped at her. The fact that he reacted to that wave like it had punched him in the gut. She’d seen his control slip for a second—just one—but it had been enough.

But… no. No, it couldn’t be. There was no way...

"Tails can’t find anything. I can’t find anything. The sensors didn’t detect a source, and Knuckles…"

Her eyes narrowed slightly.

"He’s hiding something."

But she said nothing. Not yet. Not with Tails in this state.

"Look," she said finally, shifting gears, "just… keep working on it, Tails. There’s got to be something buried in the data we missed. Maybe a new variable. I’ll keep asking around and see if anyone noticed anything unusual right before the wave hit."

Tails gave a small nod, but his eyes were glassy. Amy continued rubbing his back.

Rouge lingered in the doorway a moment longer. Something told her the answer was closer than they thought. Something told her the Master Emerald wasn’t gone, wasn’t destroyed.

It was here. Somewhere in this base. Hidden. Tied to Knuckles. She just didn’t know how, not yet.

But she’d find out. She always did.

The simulated sounds of chirping birds and distant waterfalls echoed softly through the lush little room tucked into the belly of the base. A low hum of artificial wind carried the smell of soil and dew, courtesy of some clever tech work from Tails months ago. Meant to replicate the serenity of Angel Island. A small comfort. A memory brought to life.

Knuckles was on his knees beside a pool, designed to mimic the lake near the shrine where the Master Emerald had once sat.

He dipped his hands into the water, watching it ripple around his thick fingers. He scooped a handful up, let it pour through his palms slowly, watching the trail of droplets break the surface below.

"…I know you can hear me."

His voice was low, barely more than a whisper. The stillness of the room made it feel louder than it was.

"I know you're in there. You’ve always talked to me. Even when I didn’t want you to."

No response. Just the subtle lapping of water against the stone.

"You told me I was your protector," Knuckles muttered, leaning forward to stare at his reflection in the shimmering water. "Told me I had a purpose. But now you’re just… silent."

His purple eyes stared back at him. But something was off. His brows pulled together.

The tops of his irises shimmered faintly green, like a burnished glow barely peeking through his natural color.

"…What the hell?" he murmured, leaning closer.

He rubbed at his eyes with the back of his glove. Looked again. Still there.

The same green that flared through him during that damn energy wave earlier. The same green that had made his whole body feel like it was about to split open.

Frustrated, he pulled away from the water and pushed to his feet, snatching up the bowl of grapes someone had left him on a small nearby table. He didn’t remember asking for them, but whatever. It was something to chew on.

He stalked through the corridors, ignoring the stares and the few people trying to ask him if he was okay. His only answer was a sharp grunt as he shoved open the door to his private quarters and kicked it shut behind him.

The chair groaned as he dropped into it. The bowl of grapes thunked onto the desk beside his elbow. And then—with a deep, heavy breath—Knuckles slammed his forehead against the desk.

"Dammit!"

The wood cracked faintly under the force.

"I didn’t sign up for this!" he growled into the desk, not lifting his head.

"I’m not a general. I’m not a damn beacon of hope. I’m just the guy who used to sit on a floating rock and make sure nobody stole a glowing gem. That gem being you!"

He sat up suddenly, fingers gripping the edge of the desk.

"What do you want from me?" he barked, eyes glowing faintly again, "you’re inside me, aren’t you? Hiding. Watching. Guiding or—or pushing—I don’t know! But if you’re gonna keep sending waves of power through me like I’m a walking battery, then maybe actually say something next time?!"

The silence in the room was heavy. Oppressive. Thick like a storm about to break.

"…You told me you were alive," he said softer now, eyes falling to his hands.

"You showed me. All those years. The way you hummed when I was close. The way you warned me when danger was near. So why the hell won’t you talk now?"

He closed his eyes.

"I need you," he admitted.

The words felt like swallowing fire. He hated them. Hated that they were true.

"I don’t know what I’m doing. And people are looking to me like I’ve got it all figured out. But I don’t. I’m guessing. Every day. Every second. And you’re just… hiding."

He picked up a grape, stared at it for a long moment, then crushed it between his fingers.

"…Sonic would know what to do."

The name hit him harder than he expected.

He leaned back in the chair, rubbing his face with a tired groan. "Sonic would have been up there making dumb jokes and finding some crazy, impossible plan that somehow works anyway. He always did."

He let his head fall back against the chair, staring up at the ceiling.

"…I can’t lose him."

His voice cracked.

"I don’t care if we’re in a war. I don’t care about strategies and reports and logistics. I want my mate back and you won't help me!" 

There was no answer. No hum. No pulse. No whisper in the back of his mind.

Just silence.

Knuckles closed his eyes, that faint emerald shimmer in them pulsing once before fading again.

"…You better start talking soon," he muttered. "Because if something happened to him… I’m gonna burn the world down."

Chapter Text

The robot let out a singular, sharp beep—confirmation.

Then it turned on spindly feet, the whir of its servos fading into the dim silence as it left the room. On the main screen, a sterile report began scrolling: "Chaos Energy Depletion Report: All emerald-based systems nonfunctional. Source of anomaly unknown. Emeralds inert. Retainment advised."

Eggman just stood there, silent.

The room still hummed faintly with residual static from the chaos wave, but the emeralds’ glow—their energy—was gone. It didn’t make sense. It shouldn’t be possible.

And yet…

Eggman ran a hand through his mustache, glaring at the screen as if it might reverse what just happened.

Behind him, chained and trembling, Sonic barely twitched.

The hedgehog’s shoulders were hunched low. His head hung limp between his arms. The defiance in him—the fire—was… gone. Just like that. It didn’t flicker out. It had been crushed.

Eggman turned slowly, expecting another outburst.

But Sonic didn’t even move.

"…That’s it?" Eggman asked aloud. His voice echoed too loud in the red-glow room. "No snappy comebacks? No snide little quips? You’re just going to—what—quit?"

No answer.

Eggman walked up, boots clicking, then crouched in front of the hedgehog.

"Let me get this straight," he said, voice like venom-laced honey. "I spend years trying to break you. I capture your friends! Critters! Take your world apart bit by bit. I’ve enslaved entire cities, stolen your emeralds, nearly cracked time and space. Split the moon in half! And yet still, nothing...nothing could bring you down."

He leaned in closer.

"But when the only one echidna goes missing…you crumble."

Still no answer. Sonic’s jaw was clenched tight, but his eyes had gone distant. Hollow.

Eggman laughed bitterly and stood. "You’re more pathetic than I gave you credit for."

He turned toward the console again, fingers tapping against the metal thoughtfully. The emeralds may have lost their power, but he wasn’t giving them up. Power didn’t just vanish—something happened to short-circuit their connection. Maybe interference. Maybe a device. Or maybe something—or someone—had intentionally cut them off.

He'd find the cause. Eventually.

But first…

He looked back to the hedgehog.

"You know," he said, almost conversationally, "I expected you to "fight." Even just for the idea of him. You used to be so full of that whole ‘hope wins’ crap. But look at you now."

Sonic exhaled shakily, but still didn’t raise his head.

"You thought he was dead," Eggman continued. "Fine. That happens. But I threw that chaos pulse in your face—do you know what that means? Something massive happened out there. Energy like that doesn't just occur. And still—still—you just hang there like a sack of useless spikes."

There was a low, cracked whisper then.

"…You shouldn’t have said his name."

Eggman blinked, cocking his head.

Sonic’s head slowly lifted. His eyes were bloodshot, but now sharpened to a dangerous, smoldering stare. Not on fire—but burning with something slow and dangerous.

"I was dealing with it," Sonic said, voice raw. "I was surviving. And you had to talk about him. Twist it. Mock it."

He tugged against the chains again. Not hard. Not with hope. Just… on instinct.

"You know what hurts the most? You almost gave me hope. For a second, I thought…"

His voice broke again, "I thought you found him."

Eggman didn’t answer. He didn’t need to. He could see now—his experiment had worked. Just… not the way he intended.

"I gave everything for him," Sonic whispered. "He’s my mate. He’s my soul. You don’t understand what that means."

He glared through heavy eyes, voice suddenly low and shaking with venom. "You don’t get what you took from me."

Eggman stepped back, cautious now.

"I thought watching you break would be fun," he muttered. "But this… This is just sad."

Sonic slumped again.

"Yeah," he said flatly. "Well. Guess I’m not your entertainment anymore."

Eggman lingered a moment longer, then turned toward the exit.

"Monitor him," he snapped to the intercom, "vitals, brain activity, all of it. I want to know if anything changes. And lock the chamber. Double the guard. If this thing’s turning into a shrine to heartbreak, I’d rather not have visitors."

The door slammed shut behind him, leaving Sonic alone in the dim red glow.

Still chained and still silent.

But his eyes, dull as they were… weren’t entirely dead.

Somewhere—buried deep beneath the ache and the tears and the crushing despair—there was something small and steady.

Something like a heartbeat.

A tether. A false string maybe.

Even if he couldn’t feel it anymore.

He closed his eyes and whispered, voice hoarse:

"You’re still out there, Knux. I know you are. yet, when I say it, I feel like I'm just lying to myself even more..."

Knuckles doubled over with a choked breath as that burn returned again, sharp and stabbing—just behind his sternum. The Master Emerald pulsed in his chest, unseen but there, like a second heart that had decided to beat with all the fury of a thunderclap.

He groaned and stumbled toward the desk, clutching his ribs.

"Not again," he hissed through his teeth.

It wasn’t like normal chaos interference. This wasn’t just a spike of energy. This was pain. Familiar pain. The kind only the Master Emerald could deliver when it was acting without his permission—which was rare. Which was dangerous.

His knees hit the floor.

It hit him all at once.

"That blast… it was me." He whispered to himself, lips barely moving, "that wave... the emeralds... the shutdown…"

He slammed his fist on the desk with a THUD. It cracked the edge.

Of course it was him.

Of course it was her—the Master Emerald. That pulse of power must’ve reached across continents, straight into Eggman’s base. The emeralds there—seven of them, each radiating chaos—would’ve reacted violently when the Master Emerald suddenly reasserted dominance.

Neutralized.

"But to absorb them... like that?" Knuckles muttered, fingers trembling as he sat back on his haunches. "I’ve never—she’s never—"

He paused.

A faint shimmer along his arm caught his eye.

His breath stopped.

"…What the hell?" he whispered.

From elbow to wrist, his red fur had begun shifting—shimmering with an iridescent hue that slowly, unmistakably, turned pink. Not the pale, faint pink of sunburn or some weird filter. No. Bright. Radiant. Alive.

The color of Super Knuckles.

He shot up, stumbling back and inspecting his arms, then his ankles. The transformation was creeping, slow like molasses—but constant. His limbs were glowing with super energy.

"But I don’t have the emeralds," he muttered, pacing, "that’s not how it works. You need all seven. You have to use them."

He paused again.

"…Unless I am using them."

The realization settled in his chest like a stone. His heart thudded faster. The Master Emerald hadn’t just stopped the Chaos Emeralds.

She’d taken them.

Ripped the energy from Eggman’s clutches and stuffed it directly into the only living conduit she trusted: him.

Knuckles shook his head, "no, no, no. This isn’t right. This isn’t—safe. If anyone sees this—"

He looked around, frantic. His eyes landed on a roll of medical wrap sitting near the supply locker.

"That’ll have to do."

He kicked off his shoes and immediately regretted it—the pink had started seeping into the fur between his toes. He clenched his jaw, pulled his mitt off with his teeth, then started wrapping his wrist tightly.

The moment the bandage made contact, the glow dulled—muted but not gone.

"Okay… okay. That’s something."

He worked fast, wrapping both arms from elbow to hand, then his ankles, pulling his mitts back on tight. When he slid his feet into his shoes, he noticed the faint pink glow still bled through the seams. He muttered a curse and tucked the bandages deeper down.

A knock broke the silence. Knuckles froze.

Then a shfft—paper slid under the door.

Knuckles stared at it for a second too long before walking over and snatching it up as he  read the report.

His eyes narrowed immediately. 

Another squad. Another loss.

"Zone 5," he muttered, "no survivors. One escapee with injuries. Eggman’s bots swarmed the checkpoint."

He crushed the paper in his hand before he could stop himself, then slammed his fist against the wall with a CRACK. A dent formed in the concrete.

He laughed—but there was no humor in it.

Just bitterness.

Just grief.

Tears welled in his eyes, uninvited and hot, but he refused to let them fall. He couldn’t. He didn’t get to break down. Not now. Not with everything happening. Not with Sonic gone. Not with Amy and Tails barely holding themselves together. Not with *Rouge* giving him that look like she already knew he was hiding something.

He exhaled—hard—and backed away from the wall.

"…What good is a leader if everyone who believes in him keeps dying?" he muttered, wiping his eyes with the back of his wrapped wrist.

He returned to the chair near the window, dropping into it like a stone. The base lights outside flickered in the distance. Repairs were still underway after the chaos pulse. It’d take a while to recover.

Knuckles reached for the bowl of grapes on his desk. He popped one in his mouth without tasting it. His eyes drifted to the ceiling, mind buzzing.

"Everything’s going to make sense soon," he said, almost like a prayer, "this’ll all mean something soon."

He stared at his hands—still pink beneath the wraps. Still glowing.

"…It has to."

After a while, Knuckles paced across the commander’s room like a storm trapped in a cage.

His chest felt tight, that awful energy still simmering beneath the surface like molten lava barely kept in check. The soft thrum of the Master Emerald’s power was ever-present in his body now, like a ticking time bomb wedged inside his ribs. His hands trembled, not from fear—but from restraint.

He turned to the wall and slammed his fist into it once again, not hard enough to cause damage this time—just enough to make a point.

"I should’ve never taken you off the damn island!" he growled through clenched teeth, staring at nothing, "you were safe up there! Contained. Grounded. You weren’t supposed to be in me!"

His voice echoed back at him hollowly, bitter in the quiet. The bandages on his wrists itched with warmth. The glow was still there, still wrong.

Then—

Knock-knock.

"Commander?"

Knuckles froze.

Amy’s voice.

What the hell was she doing up and about?

He quickly spun around, composing himself, adjusting the bandages under his gloves and the collar of his shirt where sweat had gathered at his neck. His voice didn’t sound right when he answered—it came out too gruff.

"…Yeah?"

The door creaked open, and Amy poked her head in. Her pink quills looked messier than usual, eyes tired but alert, "you okay? I heard yelling."

He blinked. "Uh… just talking. To—uh…" He coughed, "to myself."

Her eyes narrowed slightly.

"…You always yell at yourself like that?" she asked, stepping into the room.

Knuckles folded his arms and turned toward the desk, "only when I’m losing arguments."

Amy arched a brow but didn’t say anything. She glanced around the room, noting the scuff marks on the floor and the slight dent in the wall. Her eyes slid back to him, "Rouge sent me."

Of course she did.

Knuckles’s eye twitched. He turned sharply away from her, pretending to shuffle some papers.

Figures. The bat was still trying to play detective after their fight earlier. So now she sends the team’s emotional support unit to break him down with kindness and wide eyes.

"How’s Tails?" he asked, voice calm, but firm, "aren’t you supposed to be with him?"

Amy leaned against the desk casually, watching him, "he’s sleeping. Finally. Rouge thought I should check on you for a change."

Knuckles scoffed, "I’m not the one falling apart."

"Could’ve fooled me," she said, crossing her arms, "you’re wrapped up like you just walked out of a boxing ring. Speaking of which—"

Damn it.

Knuckles stiffened.

Amy’s gaze dropped to the bandages wrapped tight around his forearms, "what happened?"

"It’s nothing," he said quickly, "just… minor stuff. Training accident."

Her brow furrowed. "Training with what, a flamethrower?"

"Listen," he said, a little too loudly, "I’m fine."

Amy frowned, "you sure?"

He sighed, then turned to her with a lopsided grin, trying to force casual, "come on, Amy. I’m tougher than leather. You know that."

She didn’t look convinced.

"Seriously," he added, holding up his bandaged arms. "Just a few burns from some sparring drills. Training bots got a little too excited. I patched up and moved on."

Amy huffed, hands on her hips, "you could’ve told someone."

"And have everyone panic again?" he muttered, shaking his head, "no thanks."

There was a beat of silence. She looked at him with that same look she always gave Sonic whenever he was clearly being a dumbass—equal parts annoyed and fond.

"…You're such a knucklehead," she said.

Knuckles smirked, "yeah, well. I live up to the name."

Amy reached over and flicked his arm lightly, not enough to hurt, but enough to annoy, "just don’t make it worse hiding it, okay?"

He side-eyed her, he already was hiding it, then sighed, "…Yeah. Alright."

Amy let out a breath and looked around the cluttered desk, "what even is all this, anyway?"

Knuckles pounced on the change of subject like it was a lifeline, "glad you asked. I was actually about to file a report, but—" he held up a pencil, snapped at the tip, "—this damn thing broke. Again."

Amy blinked, "how hard are you gripping it?"

"I wasn’t!" he lied. "It’s just… cheap."

"Uh-huh," She plucked the pencil from his fingers with a roll of her eyes, "you need, like… special gorilla-strength office supplies or something."

Knuckles chuckled, "you volunteering to be my secretary now?"

"Oh please," Amy smirked, pulling up a chair beside him. "You couldn’t afford me."

He laughed louder, genuine this time, and leaned back in the chair as she began flipping through the report stack.

"Okay," Amy said, reading over one sheet, "this was not filled out properly. Did you forget to list unit numbers again?"

"Maybe."

"Knuckles!"

"Look, I was busy punching things. You know. My actual skill set."

Amy groaned and pulled out a pen, "you’re lucky I like you."

He glanced at her, smile softening, "I know."

For a few minutes, there was a comfortable silence—punctuated by the scratching of Amy’s pen, her mumbling as she corrected form fields and section headers, and Knuckles occasionally tapping his knuckle against the desk.

The pink glow beneath his bandages still burned. The emerald inside him still pulsed.

But, sitting there beside her—just for a moment—he felt grounded again. Like the world wasn’t falling apart.

"Thanks, Amy," he said quietly.

She looked up, surprised, "for what?”

Knuckles shrugged, "being a pain in my ass, mostly. But also… helping."

Amy smiled and gave his arm a gentle nudge, "that’s what I’m here for."

The soft scratch of Amy’s pen on the report was oddly soothing. Knuckles leaned over the table, elbow propped on the edge, palm against his cheek as he dictated numbers from memory, barely understanding them—but repeating them like a machine.

"—and twenty-four units dispatched to sector three... I think." He frowned. "No, wait. Was it twenty-four or twenty-nine?"

Amy didn’t even look up, "It was twenty-nine. You already said twenty-four for sector two."

"Right," Knuckles grumbled, running a hand through his dreads. "I hate logistics."

"You’d hate it less if you read the manuals." She jabbed the pen at a nearby filing cabinet. "They’re literally color-coded by topic. Red is for combat reports, blue is medical, yellow’s base layout, green’s rules and protocol—"

"Yeah, yeah," he cut in, groaning, "I know. You went over the system like five times."

Amy looked at him over the top of the papers, "and yet you still don’t read them."

Knuckles shrugged, "they’re boring and half the words sound made up."

She smirked, "Imagine how much easier your life would be if you just knew where everything was instead of memorizing a million random numbers."

“…Yeah. Maybe.” He leaned back and cracked his neck. "Maybe tomorrow."

Amy rolled her eyes, clearly unimpressed, and was about to start correcting the next form when she paused, tapping her pen on the edge of the table. "…Hey, what happened to the rainbow flag we gave you?"

Knuckles blinked. "Huh?"

"You know," Amy gestured vaguely, "The one from your ‘Happy Sexuality Confirmation Day’ party last month? Rouge, Tails and I worked on it for weeks. I hand-stitched that thing."

Knuckles’s jaw tensed. His gaze dropped to the desk. "…Oh."

Amy’s expression shifted, "Don’t ‘oh’ me. Don’t tell me you took it down."

Knuckles sighed, heavy and tired, "Amy…"

"Knuckles."

"…A rookie came by. One of the newer scouts. Brought a second guy with him to get orders." His voice dropped. "They saw the flag."

Amy’s face darkened. "And?"

Knuckles shook his head, jaw clenched. "It got bad."

"What do you mean ‘bad’?"

"They tore it down."

Amy’s hands tightened on the pen.

"They said some stuff," Knuckles continued, voice flat. "Loud. Disgusting. Homophobic crap. Mocking it. Me. Called me a freak for being proud of who I am. Asked… inappropriate stuff about me and Sonic. Really vulgar things."

Amy’s mouth parted, stunned. "Are you serious?"

He nodded, not looking at her.

"I… I didn’t even know what to do." Knuckles exhaled sharply, staring at his hands. "I couldn’t hit them. I wanted to. But I didn’t. I just… stood there. Listening."

Amy stood slowly from the chair, "Where are they now?"

"They’re still here."

“What?!” she shouted, furious, "Why the hell would they still be here!?"

Knuckles flinched but didn’t back down, "Because if I file something, it turns into a mess. Paperwork. Investigations. And we need every pair of hands we can get right now, even if those hands are attached to assholes."

"That’s not a reason!" Amy snapped. "You don’t let that happen, Knuckles! You’re the commander! If people think they can get away with that—"

"I know!" he shouted suddenly, louder than he meant to. His fist slammed into the desk, rattling the papers.

Amy recoiled, startled.

Knuckles breathed hard, trembling slightly. Then, in a quieter voice, he said, " know. I should’ve done something. But I didn’t. I just… couldn’t."

There was silence between them.

"I stayed in here for four days," he muttered. "Didn’t leave. Not even when someone called in for a med emergency. I let Rouge handle it. I didn’t want anyone to see me."

"…Why?" Amy asked softly.

"…Because I didn’t feel proud of myself anymore."

Amy’s chest hurt. She reached across the desk and gently touched his arm, "Knuckles…"

"I started asking myself if I even knew who I was." His voice cracked, "If maybe I was just lying to myself the whole time. I kept thinking about what they said, over and over, like it got stuck in my head. And then I thought—what if I got this whole thing with Sonic wrong? What if he doesn’t actually—"

His voice broke. He turned away quickly, covering his eyes with his forearm.

"I hate that they made me doubt it,” he whispered, "hate that I started pulling away in my own head. Like I was standing there holding a bond that suddenly didn’t feel real anymore."

Amy sat back in her chair slowly, her own expression unreadable now. She toyed with her pen, not speaking for a moment.

"…I get it," she said finally, voice quieter, "I mean… not all of it. But…"

She met his eyes, forcing a smile, "I’m still mad you didn’t tell me. But I get why you didn’t. I’d probably have burned half the base down."

He gave a weak laugh, "That’s why I didn’t tell you."

Amy reached into her pocket and pulled out a tiny scrap of rainbow fabric—something that looked like it’d been torn off the original flag. She’d kept it, tucked away, folded perfectly.

She held it out to him.

"I don’t care what they said," she murmured. "You are not less than. You are not a mistake. And that bond with Sonic? It's real. I’ve seen it. I felt it."

Knuckles stared at the scrap, then slowly took it from her, hands trembling.

"I’m sorry," Amy added quietly, voice raw, "I’m sorry they made you feel that way. And I’m sorry I gave you crap for taking it down without knowing why."

"…Thanks," he whispered.

Amy leaned back with a sigh, "Next time, you better tell me. Don’t make me find out after the fact. That’s an order."

Knuckles gave her a lopsided smile. "You don’t give me orders."

She jabbed her pen at him again, "Wanna bet?"

His laugh came easier this time. A little steadier.

"I’ll stitch a new one," she said after a beat. "This one’ll be better. Stronger. Fireproof. And I dare anyone to touch it again."

Knuckles looked down at the scrap in his hand, then back to her.

"…Thanks, Amy."

She shrugged, looking down at the reports again, "Yeah, well. You’re family. You don’t let anyone mess with family."