A/N: Thanks to your reviews, my plot bunny was fueled up enough to not only rewrite, but to also double the size of this chapter.

Please note: Character thoughts are in italics.

Disclaimer: I do not own the turtles. But I'll happily wish, beg, plead and pray until I do.

Chapter 15-Choosing Sides

The four teenagers let out a collective groan as they slowly opened their eyes.

Free of the effects from the paralyzing agent, Leonardo was the first to rip the neural interface off of his head as he leapt to his feet. The confused turtle fled from the room.

Raphael jumped up to go after him, but was stopped by Donatello's hand on his arm. "Raph wait."

Raph glared at his brother in protest. "Donnie."

"No Raph, we have to give him time."

Mikey approached his two brothers. "Dudes, did all of that really happen?"

Don turned sorrow filled eyes at his youngest brother. "I'm afraid so Mikey."

Raphael crossed his arms over his plastron as he stared at his purple clad brother. "So what now, brainiac?"

Donnie shrugged his shoulders. "The effects of the neural interface will take time to wear off. Often during a traumatic experience multiple memories are repressed. Exposure to the neural interface will trigger a cascade effect. We're probably going to be flooded with memories for a little while."

Michelangelo was delighted at the thought of more memories resurfacing. "Oh dudes, that is so cool!"

Raphael snorted at this new piece of information. "Fantastic, more surprises. I hate surprises." He smacked his fist into an open palm. "The Shredder's responsible for tearing our family apart." He hit his open palm again. "I say we hunt him down and take him out."

Don looked at his frustrated sibling. "Raph, we have no idea where the Shredder even is. Or what he is planning against the Utrom."

Before Raph could argue, Master Splinter walked into the room and interrupted. "Donatello is correct. For now, we must wait to see what our enemy's next move will be."

Raph let out a huff and stormed out of the lab to head towards the dojo.

Michelangelo was sitting alone on the couch, playing a new video game when suddenly he felt the room tilt sideways. What the shell?

**Flashback**

A young Michelangelo was hiding in the shadows as he watched his eldest brother begin his meditation. Trying not to let out a chuckle he silently crept up on his prey.

A young Leonardo took another breath in and then slowly let it out. Breathe in, breathe out. Breathe in, breathe…wait a minute, is someone in here?

Leo opened one eye and looked around the room without moving a muscle. He took another breath in, and then he heard it. The faintest shuffle of a foot along the dojo floor. Only one turtle would try to sneak up on him while mediating, and that would be his energetic younger brother Michelangelo.

Trying to hold back a huff of frustration, Leo opened his other eye and tensed his muscles, preparing to leap.

Mikey pressed onward, slowly advancing on his older brother, keeping the whipped cream pie steady in his hands. Almost there….almost there…

The orange masked youngster tensed, prepared to hit his older brother, a slow grin spreading across his eager face.

Now a foot away from his target, Mikey launched the pie, only to find himself facing empty air.

Leo heard Mikey's heavy breathing getting closer. When it sounded like he was almost on top of him, Leo used his hands to press off of the floor and leapt straight up as high as he could. Twisting he began a backflip and pushed off Mikey's shoulder with one hand, while using his other hand to tilt the whipped cream pie so that it was redirected, now aimed for Mikey's face.

Mikey let out a yelp of surprise as the pie hit home. Startled, he lost his footing and landed on his bottom.

Leonardo smiled, then let out a yelp of his own, as he landed off balance and right on his own bottom.

Laughter began to fill the dojo.

"Dude, look at us."

**End Flashback**

Mikey sat still for a moment before realizing that he had dropped the video game controller on the floor. Wow, me and Leo! Dude, that prank would have been epic! I've got to try that again!

Donatello began disassembling the neural interface devices and packing them up when he felt the room tilt sideways. What the, oh wait, it's probably a memory.

**Flashback**

A young Donatello sat on the floor with a large book in his lap and a second, even larger book off to his right. Every few minutes he would pause and turn to the second book, as he looked up the definitions in the dictionary.

The sound of a throat clearing made the curious youngster look up, into Master Splinter's smiling face.

"My son. We are to begin practice soon."

Donnie let out a sigh as he put the book down. "But Master Splinter, I'm almost finished with this chapter. Can't I skip practice for today, just this once?"

Master Splinter sat down next to his child. "My son. You have a brilliant mind. And I know that you would rather outthink than outfight an enemy. But the human world is sometimes dark and often dangerous. It is essential to our survival that you and your brothers become masters in the art of Ninjitsu. Humans often do not accept that which they perceive to be different. Our safety depends on us living in the shadows and being able to defend ourselves, if necessary."

Donatello frowned. "Hai, I know Master. But sometimes, it just feels like everyone else is so much better than me at fighting."

Splinter let out a chuckle as he picked up the book his young son was reading. He held the book up for the young turtle to see. "Donatello, do you understand the first chapter in this book?"

Surprised at the question, Donnie shrugged his shoulders. "Of course sensai."

Splinter prodded. "And how did you figure it out?"

Donnie pressed his lips together for a moment, then answered. "I spent the time looking up the words I didn't understand in the dictionary."

Splinter continued. "And what of your brothers, do they understand this book?"

Donatello shook his head before he answered. "No."

"And why is that my son?"

"Well, it's probably because…" Donatello stopped mid sentence, his eyes growing wide. He figured out what Splinter was getting at. "It's probably because I spent the time to figure it out. I practiced."

Splinter placed the book on the floor and stood. He stuck his hand out, beckoning to his brilliant son. "And that's why your brother's fighting skills are ahead of your own. You practice on your mind all the time Donatello, but you must also spend the necessary time, to practice your Ninjitsu skills."

**End Flashback**

Donatello sat down on a chair, his task of packing up the neural interfaces temporarily forgotten. Wow! My father is not only skilled at martial arts, but wise as well.

Raphael was letting his frustration out on his punching bag. Start with a left jab. Follow with a reverse punch. Finish with a left hook. Repeat. Left jab. Reverse punch. Left hook. Left jab. Reverse…suddenly the dojo tilted sideways. The red masked turtle reached out to the bag to steady himself. Oh no, here we go.

**Flashback**

A young Raphael was running through the sewers as his eldest brother called out from behind him. "Raph, wait up!"

Raph stopped and turned to glare at his blue masked brother. "What do ya want Leo?"

Leo paused to catch his breath before he replied. "I want to go with you."

Raph cocked an eye ridge at his brother. "I'm going to one of the forbidden zones. Go run along home ta Master Splinter Leo, like the goody two shoes that ya are." Finished with the conversation Raph turned to walk away when a hand tugged on his elbow.

"Raph wait. I want to see too."

He shrugged his arm out of Leo's grip before glaring at him. "Did ya here me Leo? I'm going to break one of Masta Splinta's rules!"

Leo shrugged his shoulders and gave his angry brother a small smile. "So?"

Raph paused for a moment, before a smile spread across his face. "Ya wanna break one of Splinta's rules with me?"

Leo shrugged his shoulders again, but the mischievous look in his eyes was obvious. "I'm not perfect Raph."

Raph let out a grunt of pleasure as he wrapped an arm around his brother's shoulders. "Leo, if Master Splinta finds out, we could get into a lot of trouble. I didn't know ya had it in ya bro."

Leo flashed a smile, then shrugged out of his brother's arms, and took off at a run. He called out over his shoulder. "Besides, someone's gotta keep you out of trouble, Raph. Race ya there!"

Raph let out a snort before taking off after his faster brother. I've got ya back Leo. I've always got ya back.

**End Flashback**

Raphael mouthed the words from his memory out loud as he slowly sank to the floor. Me and Leo, we were best friends?

Curious if his other brothers had any new memories to share, Mikey headed towards the lab. He entered Donnie's lab but before he could speak, Raphael walked in, a determined look on his face. Well I guess that answers my question.

Donnie looked up at his two brothers as they entered. But before he could ask if they too had experienced any new memories, the ring of a telephone echoed throughout the makeshift lab.

Raphael eyed his smart brother warily as Donnie removed an Utrom communication device from his brown bag.

A look of concern washed over the bo wielder's face as he answered. "Mr. Mortu."

Raphael and Mikey leaned in closer to their purple clad brother, trying to overhear the conversation.

"Donatello, Ch'rell's forces have begun to attack. We could use the help of you and your brothers."

Raphael was already storming out of the lab with Mikey hot on his heels before Donatello could finish his reply.

"We are on our way."

Leonardo raced through the sewers with no particular destination in mind. Eventually the frantic turtle decided it would be best to go topside, where the ground was dry and he could get his bearings. Lifting a manhole cover the black masked turtle found he was hidden in the shadows of an alley. He navigated the fire escape to the roof and continued to leap among the rooftops as he sorted through the confusion.

Stopping to catch his breath, the anxious turtle looked up and realized that he had unconsciously led himself to his favorite rooftop. He sank to his knees as his breath came in short gasps. What the shell is going on? The past 10 years have all been a lie? I really have three brothers, and a rat is my real father? Master Saki is an Utrom! And has been lying to me, using me, for all these years? What am I supposed to do? My father, no wait, the Shredder is going to be furious if he finds out that I know! But does it matter anymore? I can't stay with the Foot Clan. My whole life has just been turned right on it's shell! This can't really be happening!

Leo rose quickly and then stumbled, as he felt the world tilt sideways. What now?

**Flashback**

A young Leonardo entered his father's room tentatively. "You asked for me sensei?"

Already sitting on the meditation mat, Splinter did not look up as he ordered the child. "Kneel, my son."

Leo held his breath and knelt in front of his sensei. He kept his head down and tried unsuccessfully to sit still. Leonardo's thoughts raced. His father looked serious, yet Leo could not recall anything he had done wrong. He was confused as to why he was summoned to Splinter's room, alone.

After a short time of silence, Splinter looked up at his eldest son's face. "Leonardo, you and your brother's have the potential to become fine warriors. Already, your individual talents are beginning to emerge, and I will be adjusting everyone's training accordingly. As individual's you each possess strengths that can bring balance to another's weaknesses. As individual's you will each become very powerful, but when working as a team, you will become unstoppable."

Master Splinter paused, which caused Leo to look up. Splinter's black eyes were firm as he continued. "And every team needs a leader. Someone who can guide the four of you, to ensure that each of you do the right thing. Someone who can protect the four of you, to keep all of you safe. And if you and your brother's are in battle, someone who can direct each of your strengths, so that your enemies cannot find your weaknesses."

Leonardo wasn't sure he liked where this conversation was going, but he remained silent as Master Splinter continued.

"My son, the mantle of leadership is a tiring one. A leader has to give up much of himself if he is to be responsible for the safety, well being, and success of his team. But you are a natural leader. At tomorrow's practice I will announce to your brother's that the four of you need a leader for your team, and that leader is to be you."

Leo could not hold back a gasp of shock at his father's words. Lead his brother's? Give up himself? The young turtle wasn't sure about everything his sensei was telling him, but the one thing he was sure of, was that it was going to be a lot of work!

Splinter frowned at the miserable expression on his son's face. Splinter wasn't expecting Leonardo to jump for joy when he was told, but Splinter didn't think that Leonardo would be so unhappy either. After a few moments of awkward silence he prodded the child. "Does my decision trouble you my son?"

Leo licked his lips, not sure how to discuss the topic. He didn't want to disobey Master Splinter, but he wasn't sure he agreed with his decision. "But Master Splinter, what about Raphael? He is already the strongest and fiercest fighter among the four of us? Or Donnie, he's certainly the smartest? Or Mikey, he's already so adaptable. Why would you pick me?"

Splinter held back a soft smile. "You bring up valid observations about each of your brother's. Already you notice their strengths, put them first, while you discount your own, leaving yourself last. Leonardo you have always looked out for the safety and well being of your brother's. You are a natural leader and you are the perfect complement for your brothers."

Splinter paused and put a paw on his young son's arm. "Leonardo, I would never set you, or any of your brother's, up to fail. We will work together on your leadership training. You will have to trust me my son, as you and your brother's have always done."

Leonardo swallowed hard at his father's words. He did trust Master Splinter. And if his father thought that he was the best choice out of his brother's to become the leader, then he would work hard to prove him right. Leonardo gave his sensei a short nod of his head. "Hai, Father."

**End Flashback**

Slowly falling to his knees on the rooftop, Leonardo narrowed his eyes as he clenched his hands into fists.

Wait, it all makes sense now. Master Shredder's questions on how I feel about the orange turtle. Assigning the Elite Guard to me. He was trying to hide them from me. He didn't want me to find out the truth!

Leonardo felt his blood pressure rising and he let out a yell as he punched the rooftop with his fist. Blood began to run down the black turtle's knuckles but he ignored it.

He stole me from my family. He's lied to me and used me. All this time, it's all been an elaborate ruse. Master Shredder, no wait, Ch'rell, he is no father! He has no honor! And now he's going to try to wipe out an entire race. His own people. And I've been HELPING him prepare for it!

With his anger starting to bubble over, Leonardo growled and punched the rooftop again, this time leaving a crack in the stone.

But I can stop this. If Ch'rell's been trying to keep me from my brothers, then that's exactly what I need to do. He's always trying to get me to be a leader. Well now I'm going to be one alright. A leader for my brothers! Just like Master Splinter, my real father, intended for me.

The black banded turtle quickly stood. Fury flashed across Leonardo's eyes as his purpose became clear. All the sword wielding turtle had to do now, was to figure out how to contact his brothers again.

Across the rooftops of New York City, flashes of orange, red, and purple with hints of green, could occasionally be seen among the shadows. Donatello was running as fast as he could to the TCRI building, with his two brothers hot on his heels.

We'll have to go in through the air shaft, since the security detail will be blocking all the main entrances.

With his decision made, the purple banded turtle stopped a block away from the TCRI building and began to rummage in his ever present brown bag.

Raphael did not hide his frustration at his younger brother for stopping. "Donnie, what're ya doing?"

The purple masked turtle did not look up from his bag as he answered. "Raph, we can't go in through the front door. We have to use an air shaft." Then he tossed climbing spikes to both of his brothers. "With these. Let's go."

"Cool, it's like we are spider-turtles!"

Raphael's arm seemed to act of it's own accord and smacked Mikey in the back of the head.

"Oww!"

With a smirk, the hot tempered turtle followed Donnie, ready to begin their climb up the side of the building.

Leonardo's self-reflection was interrupted by a movement among the shadows a few buildings over. The black clad turtle rose from his perch on the water tower, deciding to follow. Could that be my brothers? The hopeful reptile didn't get very far when he was stopped by a puff of smoke appearing in front of him. When the smoke cleared the sword wielding turtle found he was surrounded by the Shredder's Elite Guard.

For a moment, the five ninja warriors stood in silence. Then the leader of the Elite Guard stepped forward.

"Leonardo."

Without waiting for a response, the leader turned and began to jump across the rooftops. Leonardo felt the eyes of the rest of the Elite Guard on him, waiting for him to follow.

Of course, they wouldn't know that I've decided to leave the Foot Clan. They're going to lead me back to the Shredder. Maybe I can use this to my advantage and help my brothers somehow?

With the beginning of a plan starting to form in his head, Leo silently followed the Elite Guard.

The sword wielding turtle and the Elite Guard had only gone a few blocks before Leo realized they were not leading him back to Foot Headquarters. An explosion sounded in the distance and they were heading directly to the source of the sound.

Ch'rell must've begun his attack on the Utroms.

As the silent ninja's approached the TCRI building, a team of Foot Ninja's stormed through the now missing front door of the skyscraper. Scattered among the debris were pieces of the materials the Purple Dragon, the Foot Clan and even Leo himself, had stolen for the Shredder. Observing the progress from behind a second wave of ninja's stood Ch'rell, outfitted in his Shredder armor.

Ten years of habit was not going to fade away overnight and Leonardo found himself kneeling alongside the Elite Guard before his old master.

Leonardo had to suppress a shudder as the Ninjitsu master spoke.

"You have chosen well my son. Come, it is time."

Leonardo rose and walked alongside the Shredder and the Elite Guard as they entered the smoking building.

Once inside the TCRI building Donatello led his brothers through the dizzying array of hallways that all looked the same.

Hoping to diffuse some of the tension Mikey started chatting. "Dudes, the Utrom really need to talk to their interior decorator."

Not in the mood for his youngest brother's chit chat, Raph gave him a quick slap to the head. "Can it Mikey!"

Mikey glared at his short tempered brother, but kept his mouth silent as they continued to race through the hallways.

Donatello led his brothers to a large room, where Utroms in hover plates flew overhead in a hurry. Everyone was rushing around, following the evacuation sequence.

Mr. Mortu turned to face the group as they entered the room. "Donatello, it is good to see you and your brothers."

He led the team to a series of monitors which showed various entry points throughout the building as he filled them in on the situation. "Ch'rell's men have already breached the first floor and will he up here shortly. We need to hold them off to complete the evacuation sequence. The building has already been set for auto destruct."

Raph was just itching to fight and smacked his fist into his open palm. All the talking was making him restless. Then he reached for his sais and began to twirl them in his expert hands. "Don't worry, we're going to give them a fight they won't soon forget."

Mikey agreed with his red masked brother and pulled the nunchaku from his belt. He began twirling them skillfully as he nodded. "Yeah, we've got your back pink squishy brain dude."

Mr. Mortu raised an eyebrow at this before turning to Donatello. Donnie was already answering the Utrom captain's unasked question about his missing brother Leonardo.

"Sorry Mr. Mortu, Leo ran off after we completed the neural interface. He may just need more time."

The orange banded turtle looked away from the security monitors as he disagreed with his smart brother. "Uh guys, I think he's already made up his mind."

Everyone looked at the screen, to see the Shredder enter the TCRI building, with Leonardo and the Elite Guard by his side.

A/N: Oh, it sounds like there's going to be a showdown coming up! Only one chapter is left for this story. And a short epilogue. Virtual Krispy Creme donuts to those who review!