Bayverse! Raphael X Reader
Author's note: Mmm TMNT angst..
Summary: Raphael believed letting her go was the right thing to do. When he overheard her missing her old life, he decided for her and pushed her away, thinking it would hurt less than staying.
He wasn’t supposed to hear that phone call.
“I know, Mom,” you started softly, curled into the corner of your couch, your phone pressed to your ear.
“I miss you so much. I—” Your voice caught, and you swallowed hard. “I want nothing more than to come home, but there’s… a lot for me in New York.”
Outside your window, Raphael froze.
He had come by like he always did—quiet, unannounced, a small smile already tugging at his lips at the thought of surprising you. You always left the window cracked open for him. Said it made things easier. Said it made him feel closer.
Now he wasn’t sure he’d ever hated that open window more.
He stayed on the fire escape, unmoving, the city noise below fading into nothing as your voice filled the space instead.
“I do love it here,” you continued, quieter now. “I really do.”
“But it’s hard, Mom. Harder than I thought it would be.”
His hand curled into a fist against the cold metal railing.
He knew you missed them. Of course you did. You weren’t from here—you had a life before this, before him. A family. A home that didn’t involve hiding in the shadows or jumping at every unfamiliar noise.
Raph swallowed hard, his chest tightening in a way he couldn’t fight off.
He never thought love was something meant for him—never thought it was even an option—until you came crashing into his life and proved him wrong.
He knew he wasn’t the ideal boyfriend. Hell, he wasn’t even close.
He couldn’t take you to the movies, couldn’t walk beside you down busy streets, couldn’t sit across from you in some fancy restaurant without worrying who might see him.
His world was shadows. Danger. Secrecy.
And yet… you chose it anyway.
You always told him how much you loved it—loved his world, loved them, loved the chaos and the quiet moments in between.
Now all he could hear was the crack in your voice.
The way you said you missed home.
And suddenly, all those words you’d told him didn’t feel as solid as they used to.
Because what if loving him meant losing everything else?
And what kind of person would he be… if he let you?
The answer came faster than he wanted it to.
Raph’s jaw tightened, his throat burning as he forced down everything clawing its way up.
He made the choice right there.
Because loving you wasn’t the hard part.
You deserved more than late-night visits through a window left cracked open. More than whispered conversations and stolen moments in the dark. More than a life you had to shrink yourself into just to make it fit his.
You deserved family dinners. Bright lights. A life that didn’t come with danger stitched into every corner.
He would only ever be the thing keeping you from it.
Raph sucked in a sharp breath, steadying himself, even as his chest felt like it was caving in.
“I’m sorry,” he muttered under his breath, though you’d never hear it.
Then, before he could change his mind—before he could climb through that window and pretend none of this mattered—
he pushed off the fire escape.
The cold night air rushed past him as he landed on the rooftop above, the impact jarring, grounding, final.
he knew he wouldn’t leave.
And just like that, he disappeared into the night.
“Babe, you’ve been zoning out, like, all night,”
you giggled, nudging the stack of weights with your foot as you leaned against it.
The weight room echoed faintly with the clink of metal as Raphael pushed the bar up one more time, arms straining before he locked it in place.
You had been talking—about your day, about something Mikey said earlier, about a show you wanted to make him watch—but his responses had been… off. Delayed. Distant.
Raph sat up slowly, dragging a hand over his face, avoiding your eyes.
“Yeah. Sorry,” he muttered.
You frowned, straightening a little. “You good?”
He nodded too quickly. “Yeah. Jus’ tired.”
Because all he could think about was you—your voice, cracking softly through that phone call. The way you said you missed home.
The way you stayed anyway.
His grip tightened around the edge of the bench.
You deserved more than this. More than him.
“Raph,” you said softer now, stepping closer. “Hey… talk to me.”
He glanced up at you then—and that was his first mistake.
Because you looked at him the same way you always did. Open. Warm. Like he was something worth choosing.
Like he wasn’t about to ruin everything.
His chest tightened painfully.
This… this right here? This was exactly why he had to do it.
Before he got too used to it.
Before you lost even more trying to hold onto him.
Raph stood abruptly, the bench scraping slightly against the floor as he stepped away from you.
You heard it in his voice.
Saw it in the way he couldn’t quite look at you.
Something in your chest tightened.
He’d thought of a million ways to do this—played them over and over in his head until none of them felt right. None of them felt fair.
The truth was that he loved you too much to say it out loud.
Too much to tell you that you deserved more. That all he wanted was for you to be happy—even if it wasn’t with him.
Knew the way your face would soften, the way your voice would turn gentle as you tried to convince him otherwise. Knew you’d fight for him.
And he was already hanging on by a thread.
“Uh oh… that doesn’t sound good, Raphie,” you said, a small smile tugging at your lips as you tried to lighten the mood, stepping a little closer.
It didn’t reach your eyes.
Raph felt his chest twist at the nickname.
God, he hated that this was the last time he’d hear it like that.
He couldn’t even face you anymore.
His eyes landed on the living room—his brothers sprawled out like always, laughing about something stupid, normal in the only way they knew how to be. A life he understood. A life that made sense for him.
“Hey, what’s going on?” you asked softly, stepping up behind him. Your hand rested gently on his shoulder.
He whipped around too fast, eyes dropping immediately—not to your face, not to your eyes—but to your shoes.
And before he could stop himself—
he flicked your hand away.
The second he did it, something in his chest cracked.
But he didn’t take it back.
He knew what he had to say.
Knew that once the words left his mouth, there’d be no fixing it. No going back. No late-night visits through your window. No soft laughs. No you.
He was the strongest of his brothers.
Even if it destroyed him.
Raph swallowed hard, forcing the words up past the lump in his throat.
“I don’t want you anymore.”
Heavy. Suffocating. Immediate.
You looked like you had the wind knocked out of you.
“Wait—what?” you breathed, your voice barely there as you looked up at him.
“I’m serious,” he said, the words coming out flat. Too flat. Like they didn’t belong to him.
Your brows pulled together, confusion bleeding into hurt. “Raph, what are you talking about? This isn’t—did I do something?”
And he hated himself for it.
“No,” he muttered quickly. “Ain’t you.”
Your hand twitched at your side, like you wanted to reach for him again—but you didn’t.
“Then what is it?” your voice cracked. “Because you don’t just—just say something like that and not explain it. We were fine. We are fine.”
He squeezed his eyes shut for half a second.
“This—us—” he gestured vaguely between the two of you, still refusing to meet your eyes, “—it ain’t working.”
Your head shook immediately. “No. No, don’t do that. Don’t just decide that by yourself—Raph, talk to me.”
Each word pulled at him, chipped away at the wall he was trying to hold up.
That’s all it would take.
So he hardened his voice instead.
You had to blink a few times to collect yourself.
Was this really happening?
Raph shifted like he was about to turn away—like he could just leave after saying something like that—but you reached for him before he could.
Your hands pressed against his plastron, grounding, desperate.
“I don’t understand—wait,” you said, your voice trembling as your fingers curled slightly against him.
For a second—just a second—he almost leaned into it.
Instead, his hands came up, grabbing your wrists, holding them in place.
He tried not to notice how soft your skin felt under his fingers. Tried not to think about how this would be the last time he’d ever touch you like this.
“I…” his voice faltered, just barely. He swallowed hard, forcing it down. “I ain’t want nothin’ to do with you.”
“Look at us, (Y/N),” he continued, harsher now, like he had to double down before he lost his nerve. “I’m a mutant. That’s all I’ll ever be.”
“It’s…” he let out a short, bitter breath. “It’s almost pathetic that you thought this could actually work.”
The second it left his mouth, he felt it—
Like something between you finally broke for good.
Your hands fell back to your sides.
Tears welled over, spilling silently, your lips parting like you wanted to say something—anything—but nothing came out.
You took a shaky breath instead.
And somehow… that hurt worse than if you’d screamed.
Slowly, you lifted your gaze to him.
At the rough edges of his scales, the faint scratches across his skin, the worn fabric of his bandana—like you were memorizing him.
Like you were saying goodbye without words.
No yelling. No fighting. No begging.
Just quiet, devastating acceptance.
You walked out of the lair without another word.
And Raph stood there, rooted in place—
feeling like he’d just torn his own heart out and handed it to you…
just to watch you walk away with it.
After that night, Raphael didn’t see you.
You didn’t reach out—not to him, not to his brothers. And that was the part that hit harder than he expected. You had been their friend before you were ever his. You laughed with Mikey, argued with Donnie, rolled your eyes at Leo.
Like you had just… disappeared.
Raph couldn’t tell them what really happened.
Couldn’t say that he’d pushed you away on purpose. That he’d torn you apart just so you’d have a chance to be happy somewhere else.
Saw the way he hit the punching bag too hard, the chain rattling violently with every blow. Saw how he got quieter—how the usual fire in him burned low and mean instead of loud.
He didn’t even snap back at Leo anymore.
That’s how they knew something was wrong.
And it didn’t get better.
If anything, it got worse.
Because time didn’t dull the memory of your face—it sharpened it.
The way your eyes filled with tears. The way your voice broke. The way you didn’t fight him… didn’t beg… just accepted it.
That was the part that made him feel sick.
Raph found himself in the dojo most nights now.
Late enough that no one would come looking for him.
The space was quiet, dim, the city noise barely filtering down. It used to feel peaceful.
He knelt on the floor, shoulders heavy, staring down at the small pieces of you he couldn’t bring himself to get rid of.
A couple of photos—edges worn from how many times he’d picked them up.
A bracelet you’d forgotten one night and never came back for.
His hand hovered over them before finally picking up the bracelet, turning it slowly between his fingers.
It looked so small in his hand.
Just like the way your voice sounded when you said his name that night.
Unbeknownst to him, Master Splinter stood in the shadows of the dojo.
He saw more than he ever let on—always had. He knew his sons better than they knew themselves. Knew the way they carried pain, the way they hid it.
Raphael had never been good at hiding anything.
The voice cut gently through the silence as Splinter stepped forward.
Raph flinched, shoulders tensing as he turned quickly, clearly not expecting anyone—him—to be there.
“Sensei,” he muttered, his voice rough.
Too quick, he shoved your things aside, like they were something shameful. Like evidence.
Like if they were out of sight, the hurt would be too.
Splinter’s gaze flicked to the movement.
“You train late,” Splinter said calmly, stepping closer, his hands folded within his sleeves.
Raph shrugged, avoiding his eyes. “Couldn’t sleep.”
Splinter hummed softly. “Mm.”
He stepped closer still, until he stood beside him, looking down at the scattered items Raph had tried—and failed—to hide.
“A restless mind is often not eased by exhaustion,” Splinter said.
Raph’s jaw tightened. “I’m fine.”
Splinter turned his head slightly, studying him.
“You are many things, my son,” he said gently. “But fine is not one of them.”
Silence stretched between them.
Raph exhaled sharply through his nose, running a hand over his head. “It’s nothin’, Sensei. Just… dropped somethin’ that wasn’t meant to last.”
The words tasted like acid coming out.
Splinter’s gaze softened—but his voice remained steady.
“Then why,” he asked quietly, “do you grieve as though you have lost a part of yourself?”
Harder than anything else.
Raph’s hands curled into fists at his sides.
For a moment, it looked like he was going to brush it off again—shut down, walk away, pretend none of this was eating him alive.
But Splinter didn’t move.
Raph let out a sharp breath, dragging a hand down his face.
“…She called her mom,” he muttered finally, voice low.
Splinter remained silent, listening.
“I wasn’t even supposed to be there,” Raph continued, shaking his head. “I just—went by to see her. Like I always do.”
“She was sayin’ she missed ‘em,” he went on, words coming out rougher now. “Said she wanted to go home. That it was hard stayin’ here.”
“Said she gave up everythin’.”
Silence filled the space again, but this time it pressed in on him.
“I heard enough,” Raph added quickly, like he needed to justify it. “Didn’t need the rest.”
Splinter’s gaze flickered slightly—but he still said nothing.
Raph huffed out a bitter laugh, pacing a step away before turning back.
“What was I supposed to do, huh?” he snapped, the emotion finally leaking through. “Just walk in there like I didn’t hear that? Let her keep pretendin’ she’s happy down here with me when she’s missin’ her whole life up there?”
“She don’t belong here, Sensei.”
The words came out quieter now.
Raph’s shoulders dropped slightly, the fight draining out of him.
The confession hung heavy in the air.
“I made it so she wouldn’t come back,” he added, barely above a whisper now. “Said things I—” he stopped himself, jaw tightening. “Doesn’t matter.”
It mattered more than anything.
“I just…” he shook his head, staring down at the floor. “I ain’t gonna be the reason she loses everythin’.”
Raph let out a slow, shaky breath.
“…She looked at me like she didn’t even know who I was,” he admitted quietly. “And she didn’t fight it. Didn’t argue.”
That was the part that broke him.
His voice dropped even lower.
“She just… left.”
Silence followed his words.
Raph didn’t look up. Couldn’t. His eyes stayed locked on the floor like it might swallow him whole if he stared long enough.
“Raphael,” he began, his voice calm but firm, “you have always carried the weight of others upon your shoulders.”
“She said she missed her family,” he muttered defensively. “She said it was hard—”
“And she also said she was happy,” Splinter interrupted gently.
Splinter stepped closer, his presence steady, grounding.
“You heard her pain,” he continued, “but you chose to ignore her joy.”
Raph’s head snapped up slightly at that.
“I didn’t ignore nothin’,” he shot back, though it lacked its usual bite.
Splinter’s gaze softened—but didn’t waver.
“You heard what you feared most,” he said. “And you allowed that fear to decide for you.”
“She was givin’ up everythin’ for me,” he said, quieter now, like he was trying to hold onto his reasoning. “That ain’t right.”
“No,” Splinter agreed. “Love often asks for sacrifice.”
“But it must always be a choice.”
“And that,” Splinter said gently, “was not your choice to make.”
Raph’s chest rose and fell unevenly, something cracking open in a way he couldn’t stop now.
“She—” his voice faltered. “She would’ve stayed anyway.”
Splinter nodded slightly.
Raph’s shoulders slumped, the fight draining out of him completely as he looked away, shaking his head.
“I hurt her,” he muttered, voice rough. “Said things I didn’t mean—things I knew would make her leave.”
His hands curled into fists again, but this time they trembled.
Splinter was quiet for a moment before speaking again.
“Do you believe she hates you?”
And that somehow made it worse.
“I thought I was doin’ the right thing,” he said finally, barely above a whisper. “I thought if she left now… it’d hurt less than later.”
Raph let out a hollow breath, his gaze drifting to the small pile of your things he had tried to hide.
“…Now it feels like I just threw away the only good thing I ever had.”
His voice cracked on the last word.
And he didn’t try to hide it.
Raphael didn’t hide the pain.
Splinter watched him quietly, the weight of his son’s words settling between them.
“Then why are you still here?”
“What?” he asked, brows pulling together.
Splinter stepped forward, his gaze steady, unwavering.
“You speak as though it is already over,” he said. “As though her story has ended.”
Raph shook his head, frustration flickering again. “Sensei, you didn’t see her—what I said—there’s no comin’ back from that.”
Splinter tilted his head slightly.
You hadn’t said anything.
You hadn’t yelled. Hadn’t argued. Hadn’t told him to stay away.
Splinter’s voice softened, but his words hit harder than anything before.
“You chose her path for her once already, my son,” he said. “Will you choose it again by deciding how her story ends?”
Raph’s chest tightened, his thoughts spiraling back—your face, your silence, the way you looked at him like you didn’t recognize him anymore.
“I hurt her,” he said, almost like a warning. “Bad.”
“But pain,” Splinter continued, “is not always the end of love.”
“It is often where the truth begins.”
Raph’s breathing grew uneven, his mind racing now.
“What if she don’t wanna see me?” he asked, quieter. “What if I already ruined it?”
Splinter’s gaze softened.
“Then you will have given her the respect of choosing that for herself.”
“But if you do nothing,” Splinter added, “then you have taken that choice from her… again.”
Raph’s head dropped slightly, something in him finally snapping into place.
This wasn’t about protecting you anymore.
And he’d let it ruin everything.
“…She said she was happy,” he muttered, more to himself than anything.
Splinter gave a small nod.
Raph looked up, eyes sharper now, something desperate flickering behind them.
“And I didn’t even let her fight for it,” he said.
Regret flooded in, heavy and suffocating.
“Didn’t even give her the chance to choose me.”
Splinter placed a hand on his shoulder.
“Then perhaps,” he said gently, “it is time you give her that chance.”
Raph didn’t hesitate this time.
Didn’t let the doubt creep back in.
He grabbed the bracelet from the floor, holding it tightly in his hand like it might anchor him.
“…Yeah,” he muttered, already turning toward the exit. “Yeah, I gotta fix this.”
And before Splinter could say another word—
Raphael leapt over buildings, barely feeling where he landed before launching himself forward again.
The city blurred beneath him as he ran—no hesitation, no second-guessing this time. Just one thought repeating over and over in his head.
Weeks of silence. Weeks of regret eating him alive.
What was he even going to say?
Did he even deserve that chance?
He just needed to see you.
Your apartment came into view, and something in his chest tightened.
He pushed harder, vaulting onto the fire escape with a heavy thud, barely slowing as he made his way to your window.
A complete, selfish idiot.
He was gonna fix it. He had to. He’d hold you, pull you close, tell you everything he should’ve said before—how much you meant to him, how wrong he was, how—
Before knocking, he leaned forward, cupping his hands around his eyes to peer inside.
Just to catch a glimpse of you.
Maybe you’d be on the couch. Maybe scrolling on your phone. Maybe—
Raph frowned slightly, shifting to get a better angle.
Slowly, his hand came up, pressing flat against the glass.
His eyes scanned the apartment again—
And that’s when he saw it.
No blanket draped over the couch.
No little pieces of you scattered around the space like there always were.
Raph’s breath caught in his throat.
His other hand slammed against the window, harder this time, like that might somehow change what he was seeing.
The silence on the other side was deafening.
The realization didn’t hit all at once.
slow, suffocating, undeniable.
You didn’t just leave the lair.
You didn’t just give him space.
Raph’s hand slowly slid down the glass, his forehead resting against it as his breathing grew uneven.
“…No,” he muttered, barely audible.
The one time he finally did the right thing—
and you were already gone.
His grip tightened into a fist against the window.
This was the choice he made.
And now he had to live with it.
