Hey this is my first offical fanfic. This a story I started several months ago, but did not continue because I kind of ,dropped off the face of the earth for a while. Then last month I came "back from the dead" (so to speak) and decided to re-write the first two chapters I made and go from there. This story has a large focas on action sequences and fight scenes, rated T for some things that will go on in later chapters

Disclaimer: I DO NOT OWN TMNT OR ANY OF ITS CHARACTERS (I WISH!), ALSO... THE FIRST THREE CHAPTERS REVOLVE AROUND AN ALTERNATE ENDING TO TMNT 2003 SERIES EPISODE "GOOD GENES PART 2". FOR THE FIRST CHAPTER, EVERYTHING FROM THE TIME THE TURTLES GET TO BISHOP'S BASE TO THE POINT WHERE LEO GRABS HIS MIC TO TALK TO APRIL IS ALL PART OF THE ACTUAL EPISODE, AND IN NO WAY OR FORM DO I TAKE ANY CREDIT FOR THAT PART.

NOW TIME TO BRING EVERYONE UP TO SPEED ON THE "GOOD GENES" EPISODES. DONATELLO GOT A SECONDARY MUTATION DUE TO BEING SCRATCHED BY THE BY-PRODUCT OF ONE OF AGENT BISHOP'S EXPERIMENTS. NOT BEING ABLE TO CREATE A CURE; LEO, RAPH, MIKEY, SPLINTER, AND LEATHERHEAD TRACKED DOWN AGENT BISHOP. BISHOP AGREED TO DEVISE A CURE FOR DON, BUT IN EXCHANGE THEY HAD TO STEAL AN ITEM FROM FOOT HEADQUARTERS. WELL AFTER FIGHTING KARIA AND THE FOOT ELITE GUARD, THE TURTLES USED A HELICOPTER TO BLOW A HOLE IN THE WALL AND ESCAPE WITH A MYSTERIOUS PENDENT KNOWN AS THE HEART OF TENGU

AND THATS WHERE OUR STORY BEGINS...


Chapter 1: Karai's Breaking Point

Karai had hit her breaking point. She stood in her Shredder armour and stared out through the gaping hole in the side of Foot headquarters tower top. Her helmet was off allowing her shoulder length dark hair to blow in the wind and her green eyes look over the grey clouded scenery of New York City. Anger boiled in her heart as she recapped in her head what had just happened a few moments ago. Leonardo, Raphael and Michelangelo had just escaped with the Heart of Tengu, the ominous pendent that controlled the Foot Mystic's power.

"Those turtles…THOSE DAMN TURTLES!" she cursed. She had taken note of the final warning Leonardo had given to her to stay away from his family. She had listened and for months she had left the turtles at peace and gone about her own business; and this is how they would repay her? By coming to find her, breaking into her Foot headquarters and stealing…FROM HER!

'So much for your honour, Leonardo' she thought as she gritted her teeth. She remembered how Leo had fled with the other two instead of facing her like a true warrior. Then it occurred to her that Donatello was not with them, although it was very likely that he was piloting the helicopter; or perhaps he doing some other sort of technologically savvy act to help his brothers steal from her. Either way it did not matter, the turtles and there rodent sensei, as well as there human friends, where all cowardly thieves. Hate flowed through her blood and rage churned within her and began to pulse though every cell of her body, Karai felt like she was going to explode. She had put trust in the turtles, trust that it was over, and that they would not seek out or come after her, but they had stabbed her in the back. Well she would not make the same foolish mistake again, she could take no more. The turtles had been sapping the life out of the Foot for years, making her look like a fool many times and getting her father exiled by the Utroms, to some ice planet in a diffrent galaxy. Then after things had finally settled down they had the audacity to come take an item of indescribable importance while her guard was down. This was the last straw, the turtles would have to be punished for what they did to her, and to her father; they had to be.

"And they will pay" she muttered to herself until she could hold it in no longer.

"I WILL KILL THOSE LOATHSOME TURTLES!" she screamed as thunder boomed around her and lightning flashed through the sky.

She thought of what she was going to do, she was going to find the turtles destroy everything they cared about, and this time she would make damn well sure there would be no mistakes; or survivors. She was going to grab them by the throats, hear them gasp for air…. and…. And then another thought flashed through her mind, one that scared her, the turtles had the Heart of Tengu. They technically now had control over the Foot Mystic's power. Although she doubted they knew that secret, but maybe they knew someone who did. Then she thought of another angle, what if the turtles damaged the Heart of Tengu or somehow destroyed it? It could bring catastrophic effects back on her; she had to get it back! Karai turned around and spoke to the four grey armoured, red caped Foot Elite.

"Get a hold of the scouts; I want to know which way their copter is heading"

"Already done" replied the Elite with the twin bladed sword. "The scouts spotted there copter leaving the city, they have a lock on it". Their tracker says it is heading west"

Confused Karai turned back to the window, sure they would flee but if they were leaving the city where would they be going?

"What are you up to Leonardo?" she muttered to herself before turning back to the Elite Guards. "Scramble a task force, I want two squads of ninja and a Shrednaught loaded on a drop ship in ten minutes! Also, get Dr. Chaplin to get a squad of our new; and technologically advanced Foot Mechs put on board. And Hurry up" she barked

"We have some thieves to behead!"

The four Elites bowed in unison before disappearing, leaving Karai alone in the wrecked, and rubble ridden room.

It had been a long journey but the three turtles had finally made it to Nevada. Leo gestured to Casey and April to stay in the copter as he and his brothers exited and headed into Bishop's base underneath Area 51. As they approached the door they were all thinking the same thing. 'Did Bishop have a cure to Don's new mutation, or was it all a set up?' All three of them were ready to do whatever it took to get their brother better again, even if it meant fighting Bishop and his men to the end. The front door opened and the turtles walked cautiously into a hanger which was occupied by a few of Bishop's black armoured commandos who seemed to be busy sorting through gear. The three turtles hesitated but knew that had nothing to fear as they proceeded. Then there gaze was dawn to the far end of the hanger. There the turtles could see two figures; one was their beloved master and father, Splinter; the other… Agent Bishop.

"My sons" Splinter called happily as he left Bishop's side to join them. "Bishop and Leatherhead have devised a cure for Donatello"

The turtles stopped when they reached their rat father, giving him a quick hug before turning there attention to Bishop.

"Hand over the item" Bishop ordered, his voice smooth and confident then his voice shifted to an almost mocking tone "Then you can get your dear brother back"

Leo looked at Splinter who nodded. Leo clenched his teeth, this did not sit well with him, but he trusted his father's judgement. Leo then nodded to Mikey, who after a short hesitation stepped forward with the Heart of Tengu in hand. He took several paces before stopping and tossing the pendent to Bishop, who caught it quickly. Bishop held the talisman in his hand for a few moments awing at it. Tension rose as the turtles and Splinter nervously awaited Bishop's next move. They all jumped when an alarm went off and a sudden static could be heard over the load speakers

"Base destruct initiated" a high pitched computer voice called through the loud speakers "Start evacuation procedure"

"This base has been compromised by your presence" Bishop informed them "You have fifteen minutes to collect your brother and vacate the premises". Bishop turned around and smiled "Pleasure doing business with you" he snickered as he ran down a vertically slanted hallway which sealed shut behind him by a large metal door.

The three turtles and Splinter breathed out a sigh of relieve as commandos ran in all directions. They looked at Splinter, who gestured to his sons to follow him.

Meanwhile in the lab, Leatherhead had piped the cure into the large tank which held the large unrecognizable, mutant Donatello.

"Leatherhead how's Donnie?" Leo called as him and the others rushed into the lab.

Mutated Don started banging on the thick see through wall of his pod as gas engulfed him. Leatherhead stepped back as the pod door opened and a blinding wall of gas clouded everyone's view. Everyone held there breath nervously as the cloud started to dissipate. Then out the pod stepped Donatello, the original Donatello, the cured Donatello! They all stood and awe as Don rubbed his eyes, after realizing he was not wearing his mask he looked at his family and mutant crocodile friend

"Hey guys" Don said weakly "What's up? No sooner had he finished his sentence that his legs started to buckle. Leatherhead rushed over to catch him

"I have you, my friend" Leatherhead said as he caught Don in his arms

Everyone gathered around in a group hug and welcomed Don back to the world. After the short reunion it was Mikey who was first to speak as he unburied his face from underneath Don's chin

"Come on Donnie, let's get you home" he chirped happily as Leatherhead began to help Don walk towards the exit.

"April, Casey" Leo called through a small mic he had pulled out of his belt. "Get the copter ready, we got Don"

"Leo!" she replied back franticly "I have picked up a flying object that just flew over us, it landed on the other side of the base"

"Maybe it is just one of Bishop's transports" Leo suggested

"I don't think so" April continued "You guys should get out of there now"

"April are you sure its not….." but Leo was interrupted when an explosion rocked the base, suddenly a whole was blown through a nearby wall, sending the turtles, splinter and Leatherhead tumbling to the floor.

They all groaned as they glanced up at the newly made entranced. Then through the dust and smoke emerged several robots which resembled that of the old Foot Mechs. However instead of being bulky with a grey and light blue pattern; these ones where more sleek with grey and navy blue armour, orange slanted eyes and a large red foot symbol on the chest. They were then followed up by about a dozen foot ninja, who drew their weapons upon spotting the turtles.

"The Foot" Raph spat as he and Leo helped each other to there feet. "This is great, just great" his sarcasm apparent as he drew his sais and twirled them in his hands.

The Foot Mechs pointed their arm cannons at the turtles, and fired…..