A/N: Hello my lovely people! Once again, here we are with the third addition of my TMNT MOVIE Sagas, and today we have TMNT MOVIE 3: SCEPTER OF SECRETS!

Yeah, there is no way this is gonna be exactly the same as what the real movie was, so I've altered it a great deal, adding my own story lines and twists to it whilst still keeping true to some areas of the movie that I actually liked. I hope you guys like what I do with it.

I OWN NOTHING! THIS IS NON PROFIT.

I hope you enjoy! This chapter is a sad one, despite being the first one, but I decided to kill your feels a little, because I'm just that evil!

Let's get on with the show!

TMNT MOVIE 3 2012 VERSION; SCEPTER OF SECRETS

Chapter 1: The Bonds of Friendship

Ancient Japan, Kyoto, 1603…

Deep within the mountainous regions of ancient Japan, a fog began to settle upon the damp earth, obscuring the many villages and forests in a thick, white blanket, just as the sun was rising in the distance. However, the calmness that had settled over the landscape was about to be shattered in a sudden instant, as screams and shouts of both anger and terror tore through the early morning air, and the sounds of galloping horses in hot pursuit startled the forests' inhabitants as they hid, either taking to the skies in a dark cloud of feathers and squawks of fear, or burrowing underneath the earth to avoid being trampled upon by the thundering hooves.

The men riding these horses were known as samurai, all dressed in their customary heavy armor as they gave chase to their convict through the trees and now trampled shrubs and bushes of the forest, cursing said criminal in their native language and waving their glistening swords in the air.

The so-called criminal gave no heed to their cursing and threats as he ran, barefooted and slightly bleeding, through the tangled vines, across shallow streams and over bushes of the fog covered forests, glancing behind him periodically as they pursued him. He let out a hissed curse as he realized they were closer than he had thought, and he tightened his grip on the wrapped object he held in his arms.

This thing, this tool sent from hell itself, was far too dangerous for any mortal to hold, even for himself. He had to dispose of it, let it never be touched by the hands of man again.

And he knew one being that could possibly help him now.

Tucking the wrapped object safely in his obi, the young man pushed himself to go faster, darting past fallen logs and weaving through vines that hung low as he finally distanced himself enough from the samurai that had become blocked off by the fallen log, and he broke through the trees, finally reaching his destination; the bottom of the mountain that was known to him and to those in his village, as The Sacred Mountain of the Serpent Youkai.

After firmly securing the long object in his obi belt, he began to climb the mountain face, deeming it the fastest way to get up there than taking the mountain path. Sweat beads poured down his face as he strained every muscle in his body to keep climbing, remembering the familiar footholds and crevices that he was able to use to climb this very mountain face several times in the past…

…he feared that this would be the last time that he would be able to pay his dear companion a visit, should the samurai catch up to him.

He climbed higher and higher, breaking through the blanket of fog that hung over the trees. He allowed himself a moment to stop and catch his breath as he looked down at the land below him. He could see his village from here, the place he had once called home, the people rising up early to tend to the rice fields, the children eager and ready to greet the day as they ran down the dirt paths, waving their toys in the air as they laughed and played together.

If he had not taken the sacred item, that village would have been no more by the break of day. Everything he had known would have been gone forever.

And so would his beloved koibioto…

The sound of galloping horses and shouts snapped him out of his thoughts, reminding him once more about his mission as he continued on his course, climbing higher and higher, earning many nicks and scratches as his hastened climb caused him to scrape his bare skin against the rough surface of the rocks, until at long last, he found the familiar flat surface of the ledge, in which lay a dark cave that lead deep inside the mountain. Taking a precious moment to regain his breath again, the young man ran inside the dark cave, wishing that he had a light of some sort to guide his path. But he knew he wouldn't have to wait for long or travel very far; his friend never ventured too deep within the mountain, for he enjoyed the sunlight. He hardly ever left the cave.

"…who dares enter my mountain?" growled a low, threatening voice within the darkness.

The young man stopped in his tracks, panting heavily from exhaustion as he stood boldly before the shadowy figure before him. "It…It is I, my friend," he called, his exhausted voice bouncing off the walls of the cave, "It is me, Kenshin."

"…Kenshin?" the voice replied, recognition in his voice as the owner stepped out of the shadows and approached the young human, staring down at him with dark, piercing emerald eyes. His long, scaly green snout spread out into a wide, friendly smile, showing the razor like teeth within his mighty jaws. His back, which was covered in jagged spikes that trailed down his spine and ended at the tip of his long green tail, was slightly hunched due to his long years huddled inside his cave, and his body had many scars from battles fought long ago, as were his claws that covered the tip of his webbed fingers on his large hands.

His hard eyes, full of mystery, past horrors and hidden secrets, softened at the sight of his human friend as he let out a low rumble from his reptilian throat. "Kenshin, my friend," he greeted warmly, but his crocodilian smile faded into a slight frown as he looked closer, seeing the fear in the lad's eyes and the tension in his clenched fists. "What troubles you, young one?" he asked softly.

Kenshin swallowed thickly. "My friend, I do not have much time left," he said, restraining the fear in his voice as he looked up at the spirit creature, "I have taken something of great spiritual from my village Headman in order to save my village from his tyranny, and now he id after my life…"

From the sleeves of his obi, he drew out the object, and he unwrapped the blanket that concealed it, revealing a long, silver metallic scepter, with a shining jewel-like stone that sat upon its top. The large reptile's eyes widened in surprise, and then he cast his confused gaze back to the human.

"Please, I beg of you," Kenshin continued, holding out the scepter as he bowed his head in respect before the mighty creature, "this is my final request. Please, protect this scepter; keep it away from the hands of man. This is the key to destruction upon possibly all of japan, so I beg of you, keep it safe. Keep my beloved ones safe…and my Koibito…"

The large creature nodded once, and he gently took the scepter into his large clawed hands. "…I promise you, my friend. I swear that I will keep this safe, even at the cost of my own life," he spoke, his heart wrenching inside from the knowledge that his most trusted friend, his only friend in this entire land, was not going to return to him. He was still so young, too young to die.

And all because he was doing the right thing.

Kenshin nodded, tears welling up in his eyes through his thick, brown bangs as he looked up to the mutant, smiling despite the pain, and the fear. No matter how many times he denied it, both to his family, his friends, and his beloved, he feared the day of his death. All things had to die sometime; it was only a matter of time.

He never thought his time would come so soon.

Unable hold back any longer, he ran up to the creature, wrapping his arms around his large waist in a warm embrace. The beast lowered himself to return the hug, his large arms encircling the human as he held him close for the final time. He could feel the boy's heart thumping against his chest in fear. His little body trembled in his arms.

He was truly afraid. If only there was some way he could protect him.

But his fate had been sealed, and he had made him a promise, a promise he would keep until his own dying day.

The two of them pulled away sharply at the sound of galloping, shouts and the scraping of metal. The samurai were coming. There was no time left. If they were to discover this cave, they would find the spirit as well.

Kenshin gazed up at his friend one last time. "Thank you, for everything. Sayonara, my friend," he said, his voice quivering as the tears spilled down his cheeks.

"…Goodbye, Kenshin," the creature lowered his head, hiding the tears that threatened to spill from his own eyes as Kenshin spun on his heel and charged out of the cave. He stared at his retreating form one last time, before turning away, retreating further into his dwelling.

Even as the tears poured down his face, Kenshin grit his teeth together and drew his sword, preparing to fight as he leapt out of the cave, and ran down the slope to meet the samurai head on.

If he were to die, he would die fighting, and with the honor and love for his people on his shoulders.

He would die knowing that, at least, they would carry on living in peace…

New York, Manhattan, 2014 (Present Day)

The brightly lit streets of the ever-moving city of New York were just as busy as usual, the many humans that inhabited this grand metropolis rushing around, their not-so focused minds set on their daily routines for their normal lives.

Or as normal as it had been for the past few months.

Four months ago, reports of people said to be 'ninjas' had patrolled and terrorized their city, dubbed as The Silent Crime Wave. That was, until an unidentified force that was not the police had finally put a stop to them once and for all, and peace had been restored once more, until three months after that, more reports of ninjas, and even robotic men and 'mutant' like creatures that were prowling the streets had gotten out, causing mad panic among the people.

But yet again, that same, mysterious force that even the police and detectives couldn't even decipher had put a stop to that as well.

In fact, it seemed that because of whatever, or whoever was doing these great deeds and acts of bravery was the reason behind the crime rate dropping rapidly. Of course, all police and detectives were furious, due to the fact that they had yet to find the source of this secretive force. But to the people, those people were a sign sent from heaven to protect their fair city.

The identity of these 'heroes' were still unknown, but they preferred it that way. For down in the very underbelly of this grand, clueless city, was where their heroes dwelled, deep within the darkest tunnels and shadows of the unexplored sewers, well hidden and unknown…

"BOOYAKASHAAAA!"

…and at times, very loud.

"Mikey! Get your shell back here so I can splatter you!" yelled a gruff and furious voice, echoing from inside the walls of an abandoned subway station, which had been transformed into a fully functional home over fifteen years ago, and was now inhabited by the most unlikeliest of families.

This subway station belonged to the four heroes-in-the-half-shells, the Teenage Mutant Ninja Turtles themselves.

Well, soon to be three ninja turtles, if Raphael had his way.

"AAAAAAAAAHHHH! C'MON, RAPH! I SAID I WAS SORRY! I WAS ONLY TRYING TO CHEER YOU UP, MAN!" cried Michelangelo, the youngest and most hyperactive of the four turtles as he ran screaming and flailing his arms in the air in panic as his older, hot tempered brother, Raphael, chased him with a wooden spoon.

"Throw a water balloon on ME, will ya?! I'm gonna slap you!" Raph bellowed back.

For the four boys, it had been a whole month after the events of the mutagen discovery. Much had happened during that time, and it had taken some time for the family to settle down again. Their greatest enemies, The Shredder and the alien race known as the Kraang, had been oddly silent these past few weeks, apart from the odd Purple Dragon robbery or a Kraang scheme every now and then, which the turtles were slowly getting used to, as well as adapting to the attacks of The Foot Bots that Shredder had created.

Other than that, life had been pretty normal in the lair. Well, as normal as a family of mutants could possibly be.

It was still early in the morning when the chaos erupted from the kitchen. The four brothers, Leonardo, Donatello, Michelangelo and Raphael had risen early for breakfast that morning before their training with their father and teacher, Master Splinter, when young Mikey had deemed it humorous to fill up a balloon with ice cold water, and throw it at his red clad brother, who was not known as a morning person and was already in a very sour mood to begin with, which resulted in the current chase around the living room, and the shrieked Japanese curse words. Leonardo, the eldest and most responsible out of the turtles, as well as the leader of their team, could only shake his head and watch everything unfold, whilst Donatello, the brightest and most intelligent out of the four, couldn't hold down his laughter as he watched his two brothers run after each other and squawk like a couple of angry geese.

Before Raph could finally pummel Mikey into the ground, the rapping of a staff upon the floor silenced them all as they stood to attention. Master Splinter emerged from the dojo, raising a furry brow at his sons. He ignored the fact that Raphael had pinned Michelangelo down, and looked as if he were about to strike him, and instead shook his head with a sigh. "If you are quite finished, join me in the dojo for your training," he said, turning and walking back into the dojo, expecting his sons to follow.

Donnie snickered down at Mikey and Raph as he walked past them, and Raph growled in response. Beneath Raph, Mikey giggled, "Poor Raphie's gonna get in trouble!"

Raph raised his angered fist again, only to have Leo wordlessly grab them both by the backs of their masks and twisting them harshly as he forced them to their feet, both of them yelping in pain as they were dragged to the dojo.

Sometimes, Leo mused, he wondered why he even tried.

Soon, the four turtles were lined up in the dojo, two on each side, standing to attention as they awaited their Sensei's commands, who looked upon each of them with a father-like fondness. "My sons," he said, walking past his sons with his hands folded behind his back, "You are truly becoming impressive warriors. But to grow as a team, you must learn each others' strengths, and weaknesses."

One by one, the turtles drew their weapons; Leonardo unsheathed his twin katana blades, Raphael twirled his Sai, Donatello spun his wooden Bo staff, and as Michelangelo flipped out his nunchaku in a flamboyant fashion, he also let out a long, disgusting belch, right into Donnie's face.

Donnie reeled backwards in disgust, coughing and rubbing his irritated eyes with the back of his hand. "AUGH! Right in my face, really?!" he cried.

Mikey only laughed. "Garlic and Clam pizza!"

Leo made a face. "Why would you even eat something like that?" he grimaced.

Splinter shook his head again before continuing, interrupting his sons' 'debate'. "This competition is a 'Free for All'," he announced, "Last turtle standing wins. Hajime!"

With that, the turtles began, with Raphael charging straight for Donatello, who was still stunned from Mikey's unpleasant surprise. "I'm still seeing spots…" he breathed in a daze, before being sent flying and hitting his shell hard against the tree in the center of the dojo by a spinning kick from Raph.

"Sorry, Donnie!" Raph mocked as Mikey pointed and laughed at Donnie's defeat behind him, "It's a Ninja eat Ninja world!" He then spun around and darted towards Mikey, who was barely able to duck out of the way as Leo locked blades with Raph instead.

"What're you doing, Leo?! I was aiming for Mikey!" Raph growled.

"What past of 'last turtle standing' don't you understand?" Leo retorted, shoving Raph backwards as he slid across the floor, taking Mikey down with a sweep of his leg.

Mikey fell to the ground with a thump, and he folded his arms and pouted. "Aw man!" he whined.

Splinter stepped forwards, stroking his beard as he watched his eldest son. "Deception, misdirection," he mused, "powerful weapons in a ninja's arsenal." He then looked down with a frown as he found his youngest son silently mimicking him and his movements. Mikey grinned sheepishly before jumping back to his feet to sit next to Donnie on the sidelines to watch Leo and Raph face each other.

Raph and Leo circled each other, their weapons dangerously poised and ready. "Looks like you've leveled up to the boss fight!" Raph mocked.

Leo only scoffed. "I'm gonna wipe that smirk off your face…permanently."

With twin cries, the two charged each other, locking blades and exchanging hard blows, until Raph knocked away one of Leo's blades. Leo only hesitated for a moment before rushing back towards Raph with a growl, flinging his brothers' Sai into the tree with a swing of his katana. As Raph rushed off to retrieve his Sai and attack again, Leo swiftly ran from behind, circled the tree, and leapt into the air just as Raph turned, only able to let out a gasp of surprise before Leo struck his knee hard into the side of his face, sending him crashing to the floor on his face.

"Well, Leo won it this time!" Donnie announced.

Raph watched with a glare as Leo walked past him, picking up his discarded katana as he sheathed them both and knelt before Master Splinter, who nodded to him in approval.

Suddenly, a low animalistic growl erupted from Raph's throat. Only the whites of his eyes were seen as his breath came out in ragged angry huffs. Donnie and Mikey watched with wide eyes. "Uh oh," Mikey gulped, "He's awoken the beast!"

Then with a yell, Raph charged for Leo again, and the blue clad turtle only had a moment to stand up and spin around before the pronged ends of Raph's Sai hooked his wrist, trapping his arm in a lock as Raph rammed his elbow into his gut, and then struck him hard in the face with his fist, sending Leo flying and landing on the ground with a pained groan.

Donnie and Mikey immediately rushed to their older brothers' side, looking down and over him in worry before Donnie sent Raph a scowl. "Raph, what're you doing?!" he barked harshly. Mikey only ignored them as he looked worriedly over Leo, putting a gentle hand on his head. He let out a small gasp as he spotted something red that wasn't supposed to be on the carpet.

"I-I didn't mean to hurt him!" Raph explained, his tone clearly panicked, "It was an accident! Seriously!"

Donnie only shook his head, still glaring at Raph with disapproving eyes. It was then that Leo finally recovered, rolling onto his back as he slowly sat himself up. All eyes widened at the sight of the thick, reddish black liquid dripping down his chin as he rubbed his aching head. "…Did you guys get the number of that bus?" he groaned.

Raph gazed down at his older brother, his emerald eyes widening in horror. What had he done? He had gone too far, that's what! They always sparred together, but never had any of them hurt each other to the point of bleeding.

Or as far as Donnie and Mikey knew, that was the case.

"We have spoken of this time and again, Raphael," Splinter snapped, gaining the attention of his distressed son, "Anger is a dangerous ally; it clouds your judgment. You need to learn to control it, lest it controls you."

"But Sensei, I wasn't angry!" Raph claimed, "I was just…determined to win!"

As Donnie and Mikey helped their older brother to his feet, the three of them made sounds of disapproval as they looked at him doubtfully.

Raph glared at them. "What?! I said I WASN'T angry!" he snarled, his temper rising and boiling once more. Donnie and Mikey seemed to shrink backwards ever so slightly, but Leo only narrowed his eyes and shook his head, the blood still dripping down his chin.

Raph let out a loud growl before throwing down his Sais and storming out of the dojo, the rest of his family staring after him as they set Leo on his feet again, with Mikey's left hand grasping his shoulder, as if afraid to release him.

Leo sighed, wiping the blood off his chin with a flick of his thumb. "I'll go and talk to him," he said, patting Mikey reassuringly as he moved towards the door, but was soon stopped by Donnie's hand gripping his wrist.

"Ah, ah, Leo. We need to get you an ice pack for your head and check out your face," he cautioned, bringing Leo closer for inspection, "it looks like it's starting to swell there. And besides, I don't think anyone should be talking to Raph right now. I think…I think he still needs some time to…y'know…"

Looking down briefly in recognition, Leo nodded in acceptance, letting Donnie lead him out of the dojo by his wrist.

Watching them leave, Mikey looked up to his father, his big blue eyes full of worry. "Sensei? Do you think Raph will ever…y'know…" he stammered, looking unsure of what to say now as he played with the wrappings on his wrist.

Letting out a soft sigh, Splinter placed a hand on his youngest sons' shoulder, making him look up at him. "In time, Michelangelo, he will," he said, "I know from experience that the loss of a loved one is indeed very hard. The memories will hurt, and the pain will never truly fade, but in time, the wounds will heal."

Mikey nodded once, looking down at his feet again sadly. "…it sucks losing a friend, huh Sensei?"

Splinter nodded. "Yes, my son. It does."

Leo paused at Raph's door, staring at the metal barrier that separated him from his currently brooding brother. Preparing himself for the worst, he rapped on his brother's door with his knuckle, his other hand used to hold up the ice pack on his swelling cheek. "Raph? You in there?" he called.

"Go away, Leo!" came the growled response, "I'm not in the mood for another one of your damn lectures!"

Leo closed his eyes, taking in a deep breath through his nose and releasing it in a controlled sigh. This was not going to be easy, but it had to be done, for all their sakes.

Especially Raph's.

"Raph…just let me in," he said gently, pressing his forehead against the metal door, "I promise I won't lecture you, I just wanna talk. Please?"

A long silence passed, nothing moved, nothing stirred, and no one spoke. Leo sighed again, turning to leave, when he heard the door open, revealing the dejected form of Raph as he looked up at him with despondent eyes. He looked at the ice pack on Leo's cheek, and he turned away again, muttering a Japanese curse as he sat back on his bed, folding his arms across his plastron as he stared at the empty crate next to his bed. Leo's shoulders slumped as he moved to sit next to Raph, setting the ice pack on the bed as he looked at his younger brother. "…Raph?"

Raph slid his green eyes back at Leo, then back to the crate. "…listen, Leo," he began quietly, "before you say anything, I…me…ugh, well I'm…um…" he shrugged uncomfortably, "…sorry."

Leo smiled softly, choosing not to press further like he usually would have as he only nodded. "It's okay, Raph," he said.

Raph nodded back, still not looking at Leo. "I…I really wasn't trying to hurt you, man. I don't know what happened. I guess I'm just…I'm still…"

"…you're still bent up about Spike." Leo finished for him.

Raph hunched his shoulders, clamping his teeth shut as he stared once again at the empty crate.

It had been over half a month ago. Raph knew more than anyone that all things died in the end; it was only a matter of time.

He just didn't expect Spike's time to come so soon.

He knew the little turtle was sick, but he never thought he was that sick; just another cold or something, if normal turtles could even get colds. He thought he would be fine if he left him to rest on his bed for a little while, so he pet him goodbye and set off after his brothers.

Raph didn't cry when he came home from patrol that night to find his pet turtle lying cold and motionless on the floor; he only panicked. He didn't cry when Donnie had told him that his pet was dead; he only ran into his room and slammed the door shut, and even in the privacy of his room, he still refused to cry. And on that dark, gloomy night where he had to bury him in Central Park, he still refused to release the tears.

But it didn't mean it didn't hurt that every time he turned to look at his bedside in the morning, he was met with nothing but an empty bed in an empty crate…

Ever since his death, Raph's temper had risen more and more; the only way he could deal with the loss was to get angry, hit something, or in most cases, hit someone. He couldn't really expect his brothers to understand what he felt; they had never lost a friend like Spike before. Spike understood him like no one else did, even though he couldn't speak.

Spike was his best friend.

Leo gazed at his younger brother sadly, bringing his left arm up to wrap it around his shoulders and bringing him close. Surprisingly, Raph didn't resist the gesture, which for the hotheaded turtle, was unusual, for he was never used to being shown or showing such affection. Despite that, Leo decided to go onwards. "Raph…I really am sorry," he spoke softly, "and I know I won't be able to ever truly understand what you're going through, but trust me when I say, that the best thing you can do right now to deal with the pain, is to do what Master Splinter always does when he misses his family from the past."

Raph slid his eyes over to him. "…what does he do?" he asked quietly.

Leo smiled softly. "He focuses on the friends he's surrounded by right now; meaning us, April, Casey, Irma, and everyone else we've come to know. You still hang out with Casey a lot, don't you? You know you can always talk to him about anything, or just go 'bash some heads' with him, right?"

Raph looked to the side in thought. It was true; he and Casey had formed a strong bond with one another, the same time had found Spike in that barn over four months ago. Heck, he was like the twin(ish) brother he wished he had. He and the black haired human could do almost anything together, and whenever they went out, Raph felt all his anger and bitterness almost ebb away. Casey helped him channel or release his anger in a way that the others in his family couldn't. Casey understood him in a way that his brothers didn't.

They were best friends, just as he and Spike had been.

Leo held him closer slightly. "Don't hold all this inside yourself, Raph. Casey's there for you. We're all here for you. Don't forget that, alright?"

Raph nodded, feeling a lump form in the back of his throat. Leo saw the tears starting to appear, just brimming in his eyes, but he said nothing of it.

He would let them fall in his own time.

Suddenly, a happy cry from the living room shattered the silence between them. It was Mikey; apparently they had a visitor. Leo turned back to Raph, his arm still wrapped around his shoulders. "You wanna come out yet?" he asked.

Raph shook his head. "…not yet. I'll come out later. Gimme a minute…"

Leo nodded, gently releasing Raph, gently patting his shoulder before he stood up to leave, but was stopped when Raph suddenly lashed out and gripped his wrist, making him turn back to him with a raised brow.

Raph refused to look at him, but he did manage to mutter something. "…thanks, man."

Leo smiled. "No problem. That's what brothers do," he said as Raph let go, and he exited his bedroom, shutting the door behind him as he went to go greet their visitor. Behind the shut door, Raph smiled.

Maybe his brothers did understand a little after all…