War of the Shadows

BY Willowfly

A/N: I really didn't like Fast Forward… actually, I hated it with a fiery passion. So this story came to me in a dream one night while I was angsting over the complete failure the FF season. I soon found myself contemplating about ways to link the future of FF with the alternate-reality that is SAINW. The story got a little away from me since, but I do try to stick to that general theme.

This is my first fan fic ever, so the writing may be shaky in parts. Please be patient, all errors are in the process of being corrected.


The turtles are stuck in the future, aching to return home. Donatello works endlessly on a way when a call from the now President Bishop sends them on a mission to save not only the Earth, but the entire universe.

In the future, they walk amongst the people, no longer banished to the darkness. But still they find themselves living in the shadows—the shadows of war, the shadows of those they admire, the shadows of ghosts. A tale of unwavering hope, unimaginable pain, the injustices of war, and the scars it leaves behind.

NOTICE: Story is STILL under reconstruction. Bear with me .


Chapter 1: A Window and a Door

The engine hummed with brilliant electricity as its huge metal frame charged to life. Donatello could feel that same fluttering energy in his veins, as if the air had turned electric. He took a step back when the surge hit the receivers like a lightning bolt, a sudden pulse of light twisting through its center. The anticipation was deadly.

This just might work he thought, he prayed. He'd failed enough already.

He looked over to Cody, standing in the corner with his arms folded. His sad smile told it all: he didn't want them to leave, but knew that someday all too soon, they would return to their time, the world where they belonged. Every bit of his greater judgment told him it was unnatural to have them here, but over time, painted by the stories of his grandmother's wild tales now made tangible by some twist of fate, they had become his family—the only friends he had ever known.

And soon, they would leave him and he'd be on his own again, alone, just the same as it always has been. Each day spent working with Don on the Time Portal was like saying another long goodbye.

"If I have the calibrations set just right, I think it might be able to withstand the amount of energy required to create a viable porthole," Donatello said excitedly, childish hope flashing in his eyes. But along with the hope dwelled a premature echo of longing. Sometimes, it felt like he'd been born one hundred years too soon.

The machine's humming grew louder as a sudden pulse of energy shot through the machine, the light growing from each receptor formed another spark in the center of the frame that concentrated, twisted and grew.

Don's eyes widened, his heart raced, the joyous beat of victory. I did it! I really did it!

After a few moments, the spark grew and opened, ripped through the air like a paper cut until it was no longer just a spark, it was… home. He could smell the city air, feel it on his skin, hear the quiet sound of a car alarm echoing in the distance.

The porthole had opened onto the rooftop by the water tower where the brothers had spent much of their nighttime crusades. Many workout sessions had been drilled into them by the well-meaning Leonardo. Many nights spent just sitting, looking at the darkened sky, and feeling free for just one moment.

They had battled the Shredder there, the night they'd thought he had been dead for good, only to find they had been so gravely wrong. His heart ached for the memories—the feel of a midnight run, that eerie glow the streetlamps cast in the rain, even the sound of water rushing through the old copper pipes as he slept at night. That one little rip, that one gaping tear into the time where he belonged was enough to remind him: in the future he had gained a lot, but he had left so much more behind.

All these thoughts flew through his mind as he stared into the twisting little window. The memories that flowed over him like water felt like they were from another life, somebody else's memories haunting his own. It was a way of life forgotten by the world far too long ago. An entire century had come and passed, built on the foundations of the past, but like a void in the future's memory.

It was a time before peace, and few people liked to remember it.

Don flinched out of his reverie as the window collapsed like a caving wall. In just a breath, it was blown out of existence like a candle's flame. He blinked at the sound of the engine struggling.

"It's overloading!" He yelled over the suddenly monstrous noise. "We need to cut the power!"

Cody moved quickly to the failing engine, flipping open the compartment that housed the main power supply. But it was too late. The light in the porthole grew intensely brighter, and then, with a loud bang, it went out.

"The system's fried," Cody said, choking on the smoke coughing from the machine's underbelly. The once intricately woven web of wires now looked like a pitiful jumble of melted charcoal. "What happened?"

"I could have sworn I had it right that time," Don mused. This was the fourth overload this week. He couldn't possibly become that sloppy. "I was sure of it. We were so close." He shook his head, frustration raking at his brain. Then suddenly, his expression shifted. He remembered the air, the sounds of the city. He beamed excitedly. "I could see it! I could see New York! I mean, I could see my New York. Gosh, if only I knew what went wrong."

Cody, looked a little less thrilled, brushing ashes from his hair with a half-hearted smile. "Yeah, that was great," he said. "So close. Maybe we'll get it next time."

A noise behind them caught their attention. Raphael had appeared in the doorway, looking shaken. He stared at the mangled porthole, his hands balled in white-knuckled fists.

Don's expression sobered. "Sorry about the noise," he said, hoping Raph would spare him from whatever he head in mind.

"I don't care about the noise, Don," he said gruffly. "I'm sick of waitin' for this hunk of junk to work." Raph didn't raise his voice, but the look in his eyes was dangerous. Don braced himself for the worst, taking little comfort in the fact that Raph didn't have his weapons.

"Raph, I'm sorry. I know you're anxious, but we're getting really close and we're doing everything we can."

"Close ain't good enough!" He yelled. That pent-up frustration was looking for an out. "If you can't make that piece of shit work, than I will." He picked up a wrench lying on the floor next to Cody and hurled the heavy tool at the machine.

Don thought of throwing himself in the line of fire, but knew that it wouldn't have been worth the injury. So he stood, helplessly watching as the metal object careened toward the machine and struck it hard with a clatter of fractured metal.

"Well if it wasn't broken before, it is now," Don sighed. He didn't want to start any trouble, but he was just too upset to keep silent.

Instead of retaliation, Raph seemed disheartened. "Yeah, whatever," he grumbled, turning for the door. "Be grateful it wasn't you, Brainiac."

As he slammed the door behind him, Cody couldn't help flinching. A familiar pang of guilt leaped into his stomach. He had been the one that brought them here. It was his fault they were miserable.

Most of the time, Cody thought that the turtles enjoyed being with him, enjoyed the opportunities he presented them. For the first time in their lives they could walk in the daylight without fear. They could experience peace and acceptance unlike anything of their time. They could actually live a normal life according to the future's standards. In their time, there just wasn't any acceptance for sentient non-humans. Earth society just didn't have that kind of understanding. In their time, all of this would have been impossible.

Don and Mikey had always seemed happy. Every day they discovered something new that amazed them. The technological advances that had taken place over the last one hundred years provided Michelangelo with endless hours of entertainment and Donatello with an entire world of ground-breaking technology and new levels of understanding in every aspect of life. Cody always believed that for the two youngest turtles, living in the future was like one big amusement park.

For Leo and Master Splinter, adjustment came slowly, but unprotested. He had never heard either of them complain about anything major, so he'd always assumed they were happy. And if they were happy, Cody was very happy.

But then there was Raph. The others told him that was just how he was like. Give him some time and he would come around eventually. And it was true, for the most part. After a couple weeks he started acting more like himself, but he still seemed to be fighting this every chance he got.

Cody had tried everything to cheer him up. The races, for one. When Raphael got back on that motorcycle, he'd thought everything would be fine from then on. But in the end, nothing really changed. If anything, it only reminded him more of the past and they were right back at square one again.

It was mostly because of him that Donatello had been so adamant about repairing the Time Portal as soon as possible. They worked on it for every day, but to no avail. Progress was slow and Raph's patience was quickly wearing thin.

"Higher. Strike higher," Leonardo demanded, feet apart, crouched in a defensive stance. They'd been sparring endlessly all morning.

"I'm trying!" Mikey huffed. He was posed for another strike, but fully intended to stall until he could catch his breath.

"No you're not," Leo said coldly, taking advantage of his brother's hesitation to deliver a strong blow to the chest. Mike took it without flinching, shuffling a few steps backward. Mikey seemed to be just not getting it today. He had to snap out of this, and fast. "Don't just stand there," he demanded, "counterstrike!"

Mikey's confidence was wavering. Instead of attacking, he just stood and stared at his older brother, shaking his head as if he couldn't even remember how to execute a simple punch.

Ever since he had vowed to train harder and stop being so easily distracted by his videogames, Leo had been coming down hard on him. For over a week, every morning seemed to start like this. After just a few hours of training, Leo was easily able to wear him out.

"Okay, stop," he said dejectedly. He was trying not to let his frustration get the better of him, but seeing his brother give up so easily was ridiculous. He never even had to withdraw his weapons. Leo lowered his hands to his sides and stared at him sternly.

Mike was obviously shattered, his eyes were wandering around the room, refusing to meet his gaze.

"What have you been doing the past two weeks?"

Mikey's eyes settled on the ground as he spoke. "I've been working really hard, honest. It's just not working." He sighed, letting his shoulders sink with his exhale. "I dunno… I guess I'm not very good, huh?"

"Don't ever say that!" Leo exclaimed. It was a shock to hear Mike actually put himself down. He used to be so sure of himself, cocky, even. Leo couldn't believe that Michelangelo, the ever-so-irritating Battle Nexus Champion, would ever even dare say such a thing. "You can so much better than this. I've seen you do it. Remember your rematch with Kluh? I've never seen anyone fight like that before."

Mike shifted uneasily. "You know I don't want to talk about that, Leo."

Leo sighed, letting some of the tension drain out of his shoulders. "Look, Mike. You're a natural, but you let that carry you through too often. And sometimes, just being a natural isn't enough. If you would just practice more often, you wouldn't have let yourself go so badly."

But things had changed. Their lives weren't how they used to be. Being able to walk about in broad daylight had opened new doors for them, and Mikey was sure as shell going to take advantage of it. They could finally lead a normal life… or at least, as normal a life as a mutated turtle from the past could have. Before, all there was were sewers… his brothers… ninjitsu. But now he had the whole world as his playground. He could go wherever he wanted, do pretty much anything he wanted, even talk to anybody he wanted and nobody was ever afraid of him. He could see movies, eat at restaurants, and even walk into comic book stores whenever he felt like it and never have to worry. His life was no longer just about being a ninja, it was about being a teenager—a real teenager, not just some warrior who happened to be teenaged. It seemed right to make the most of it, unlike some brothers who were still stuck in the past.

It was funny how Leo and Raph were alike sometimes. Not that either one of them would admit it.

Unfortunately for Leo, Mikey often found himself abandoning practices or whatever because he had better things to do. A lot of times he felt guilty that his new life meant ninjitsu was taking a back seat. But for the first time he could ever remember, he felt happy, not just making the most of things, but really, truly happy. He just couldn't deny himself that.

Leo didn't understand, and in a way, Mikey pitied him for it. Leo seemed to fit in the future like an apple in a crate of oranges. While those oranges threw this awesome party, the apple just kind of watched and smiled in its weird little Leo way. But Leo wasn't an apple as much as Mikey wasn't an orange. Even in the future, ninjitsu was all Leo had. It may still be Leo's life, but it was no longer his.

"Why do you even care so much? It's not like the old days. There isn't anything to be afraid of. We don't have to fight, we don't have to be scared of being somebody's science project, we don't have to be anything but who we want to be!" Leo looked unimpressed, but said nothing. Mike shot him his best innocent grin. "Stop being such a worry wart. These are better days, bro! Ease up, go outside, see the sights! Have a little fun for a change."

"Fun? I have fun. But there's a proper balance between recreation and discipline, Michelangelo."

Mike snorted, jabbing his brother playfully in the arm. "Recreation is not fun, Leo. It sounds like polka night at the old folk's home. What do you do that's even close to fun? Come on, tell me. And meditation, training, or that yoga thing you do doesn't count."

Leo did not like the tables turned. It was his turn to shift uneasily, crossing his arms over his chest. "I enjoy those things, Mikey. Just because you don't have the patience for them doesn't mean I can't think they're fun. But other than that? I sketch. You know I sketch a little, along with my calligraphy. I just haven't had the time. Plus Cody told me paper goods are rare, so I don't plan on indulging myself. I guess that doesn't count."

Mikey's grin grew wider. It was rare to see Leo stumble over his words. "Nope. Doesn't count. See, Leo? You're missing out!"

With his lecture was lost on his brother already, the frustration was slowly creeping back in. Leo shook his head. "That's beyond the point. You goof around all day long like you've forgotten all of your discipline. If you forget everything you've ever known, how will you be able to defend yourself?"

Mikey only laughed, dealing his brother more playful jabs, but Leo only frowned. He looked so serious with that crease in his brow, and Mike was determined to end it. He jabbed his brother in the arm again. "Oh, come on Leo, you're a big stick in the mud and you know it. Lighten up for a change!"

That only seemed to make him madder- or, about as mad as Leo could actually be, which really wasn't so much mad as cold. "I'm not a stick in the mud. I'm just trying to keep you from forgetting that there are threats out there, just looking for a chance to hurt us. It might not be fun to think about, but you can never ignore it."

Mikey snorted, rolling his eyes. "See, there it is! Old stick in the mud Leo. This is the future, dude! It's awesome! No Foot, no Shredder, no Bishop. Or, well, there is a Bishop, but not a 'I'm gunna cut you open because I'm cool that way' kind of Bishop and—"

"Okay, Mike, that's enough." Leo interrupted, holding up his hand for silence and still looking very unimpressed. "Let's spar one more round, and try not to lead with your elbows this time."

Mike smiled sheepishly, twirling his nunchaku. "Does that mean you agree with me, or is it just an excuse to get me to shut up?"

Dodging the first attack, a strike with the nunchaku that listed a little too far to the left, he had time to ponder before the counterstrike. "It means… I don't know. It means I need more time to think about this."

After three well executed kicks, Mike looked like he was gaining confidence. He swung low with his nunchaku, missing a blow to his brother's knee by mere inches. Leonardo flipped swiftly out of the way and landed a few feet ahead. For the first time in a long time, he looked pleased.

Quickly, he nodded his younger brother a bow and unsheathed a single katana, holding it erect in a defensive stance.

Mikey had returned the bow, and his smile grew wider as he spun his nunchaku. "Getting better?" He grinned.

"Getting better."

In a flurry of weapons, Mike's strikes turned into a blur of bone-crushing force. But still, he was too slow. Leo blocked every one of his attacks with his katana then struck out, his sword colliding with the chains of Mike's nunchaku before it could taste flesh.

In a moment, they were locked, staring into each other's eyes.

"So how long are you going to think about this?" Mike asked teasingly. His gaze still burned with that same mischievous fire. But still, Leo was puzzled. He didn't answer. Mike's eyes searched the room, then settled back into his brother's gaze. He hesitated. When he spoke, his voice had lost all trace of humor. "You… you do know we're not ever going back, don't you?"

Leo's heart sank like a rock, but he didn't let it show. Instead, he let his eyes narrow. It was better to appear angry than heartsick. He'd covered it up well enough thus far. It would be a shame to let it show now.

"You don't know what you're talking about," he said dryly, breaking free of the block, but waiting for the counterstrike.

Mikey's grin had disappeared for a moment, but then returned, sadder than before. "Sure I do," he said with that strange little smile, "Don can't fix that thing, he's been at it for months and maybe… maybe it's better we don't go back."

Leo's eyes widened, but he covered it up with an attack. In a flurry of steel, they were locked in battle once again.

Strike with the katana, block with the nunchaku's chain. Kick, twist, miss, strike again. Another strike with the nunchaku, easily dodged, strike with the katana once again.

They sparred until they had forced each other apart, panting and sweating, weapons at the ready on either side of the room. Mikey was fighting the best he had all week.

"Like I said," Leo panted, "you don't know what you're talking about. All Don needs is more time. He can fix anything. We'll be back home soon, so we'll have to be prepared."

Mike struggled between breaths to say what he'd been dying to say all morning, all week, ever since Don started working on that time machine. "What if I don't want to go back? Did you ever even ask about what I think?"

Leo looked stunned. He stood there, mouth hanging open unabashedly like his youngest brother had just said the most horrifying thing in the world. Before he could blink, Mike was swinging those nunchaku in his direction. He had to physically shake himself to respond.

"How can you even think something like that?" He hissed through gritted teeth, swinging low with his katana. Just in time, Mike dodged out of the way. When he went to strike again, he saw something strange ablaze in his younger brother's eyes.

"Well maybe I like it here," Mike said with a frown, dodging yet another attack. "I mean, come on. It's like, for the first time in our entire lives we're finally—"

Leo attacked, cutting him off before he could say it. He didn't want to hear this. He didn't need to hear anymore.

But Mikey flipped easily out of the way, landing on the other side of the room. "…free."

That last word had him shaken, seized up every thought or trace of emotion he had inside. It was like standing as that proverbial deer in the headlights, just watching, waiting for that awesome moment of complete and udder doom.

"Wait… what?" He stammered, still trying to keep his mind focused on the attack.

"I said maybe I like it here. Maybe I don't want to go back."

Mike was standing there, twirling his nunchakus, and for some reason, the sight of his almost smug confidence, those words… maybe I don't want to go back…, they just kept replaying in his head.

Until now, Leo supposed he hadn't realized how strongly he felt, how angry he was at the sound of those words in his brother's mouth. It felt… hopeless.

Something foreign broke inside of him and he was moving in for an attack before he could feel it. It was rage. He couldn't stop himself. Before he even realized what he was doing, he was striking out with his katana, heading straight for that weak spot he'd been seeing all week, right where he would never see it coming…

"Holy shit!" Mike squealed, his eyes wide and frantic. He spun his nunchaku and let them collide the way Cody had showed him.

The tech weapons converged into a shield. When the katana collided with the force field, Leo met his brother's eyes, panting, beads of sweat running down his face. Mikey only blinked.

"I don't know what's happened to you," Leo said darkly, "but this has got to stop. You can never assume that everything will be safe forever. You can't assume we're never going back. We don't belong here, we never have, and when we go back, just remember everything you just told me, every practice you skipped, every meditation you botched when the time comes and you are not prepared."

Mikey could only stare into his brother's eyes. Their usual amber coolness seemed to be ablaze by some hidden fire. In the awkward silence, Mike let down the shield and belted his weapons, Leo lowered his own. But Mike still didn't back down. He folded his arms over his chest and glared stubbornly without a word.

Sheathing his katana, Leo didn't look away. Regaining his composure, he said in an icy tone, "Mike, give me your nunchaku."

Mikey's eyes widened and he let out a small, terrified gasp. He placed his hands over his nunchaku and gazed miserably over to his sensei sitting placidly in the corner.

"Master Splinter!" He moaned.

The old rat gazed up from where he had been sitting, silently watching the two brothers' sparring match. Looking much older, grayer, more feeble than either of them remembered, he said nothing. He looked over to his eldest son and gave a solemn nod.

"Hand them over, Mikey," Leo demanded.

Mike couldn't take his eyes off of his sensei. "But…"

"Do as your brother has told you, Michelangelo," said the old rat, looking more aware now.

Like tearing away a part of himself, a limb, a piece of his soul, he surrendered his tech nunchaku to his brother's outstretched hands.

"You need to stop relying on technology to win your battles for you. These weapons make you weak. They've made us all weak."

Mikey's nunchaku in hand, Leo stormed toward the door, turning back to Mike to shout something over his shoulder. "Go get Don and Raph and tell them to meet me in Cody's trophy room… now."

"Ok, ok, you don't have to be so pushy," he grumbled, heading out in the other direction to check the lab for any sign of Don. He had no idea where Raph would be, but he knew he would have to find him ASAP, or 'Fearless Leader' would be royally pissed off… or at least, more than he'd already seemed to be.

Mike couldn't fight away the feeling that he was in some serious trouble.

"What makes him think he's so great anyway?" He mumbled to himself. "He bosses us around twice as much as he used to. Doesn't even care about a thing I say. Take my chucks… what a jerk."

But then a thought struck him. Master Splinter had been so quiet for weeks now. It'd been a really long time since he had done any real teaching. He hadn't sparred with any of them in so long, and now he wasn't even saying anything. He was just watching, watching… Leo. Leo had been doing everything, leading meditation, giving pointers (and lectures), he was even was doling out punishments now.

Mikey shook his head. "Jerk," he mumbled again, feeling naked without his weapons.

Even Cody had become his new student, though all of them had once taken a vow to never teach ninjitsu to anyone after their mishap with Casey so long ago. He had refused to teach April, after all. But Leo had taught Cody everything he knew. Every morning he'd been giving the kid lessons on the roof before Mikey's routine shell-kicking. It seemed like recently Splinter had taken a huge step back in everything, leaving it all up to Leo.

No wonder he was being such a killjoy.

There was a noise coming down the hall from the Lab, a loud humming and then an ear-splitting explosion. Mikey could hear Raph and Donny arguing, then a smash and clamor of metal. Mike couldn't help smiling. "Raphie's up to his old tricks," he chuckled, running toward the source of the commotion.

When he came closer, he was almost bowled over by Raph rampaging out of the room like a bull and slamming the door behind him.

"What's the problem, Raphie boy?" He giggled. "Big 'ole Donny scare you?"

"Shut up Mikey. I'm not in the mood."

"Leo wants you in Cody's trophy room ASAP."

"I couldn't give a flying fuck what he wants," Raph growled.

"Whoa. Ok," Mikey said backing up a step, trying not to provoke his hothead brother any more than he already had. "Just chill, okay?"

Raph had his back to him, storming quickly down the hall. "Piss off."

"Where you going?"


"OK… have a nice time, then," he said with overdone cheer. "You can deal with Leo when you get back. You know he stole my 'chucks?" But there was no reply. Raph had already disappeared down the hall.

Shrugging his shoulders, Mikey pushed open the door to the lab and was immediately engulfed in a thick wall of smoke. "Dude, that's rank! What happened in here?" He coughed, waving a hand in front of him. He could barely see a thing. He squinted at the shape he assumed was his brother and crinkled his nose. "It smells like burning plastic in here."

"The Time Portal went into systems overload. We completely fried the matrix and… I think Raph took out a receptor. I thought I had it calibrated to withstand the necessary energy requirement, but the generator went into overdrive. The converter overheated and, well, exploded."

"Uh-huh," he said dully. The techno-jargon had apparently gone way over his head. "Then I missed it blow up? Awww… tell me next time. I wanna see!" He pouted, only half joking.

"These things happen Mikey," Don said, wrenching open the control box and examining the machine's tangled mess of fried wires. "More often than I'd like them to. It's not like I plan on making things explode."

"Well it would be cool if you did. You could be like the guys on Myth Busters!"

"Um, yeah. Do you need something?" Don blinked as a pang of fear rushed over him, terrified that his little brother just might want to 'help'. He immediately started thinking of a million reasons why he shouldn't, preparing to defend the lab with his very life if it meant he could spare it from the walking natural disaster that was 'Hurricane Mikey.'

"Leo wants you in Cody's trophy room."

Don looked relieved. Mikey had no idea why.

"What for?" Asked a voice from behind the cloud of smoke. Cody's silhouette appeared shrouded in gray ash.

Mike shrugged. "I dunno." Then, pouting, he moaned, "but he took my 'chucks!"

"Come on," Don chuckled with a warm smile, peeling himself away from the unfortunate demise of the Time Portal and throwing an arm around his brother's shoulders. "Let's find out what he wants."