In the Lair, Splinter, the turtles, and the girls were all meditating.
"We have faced many adversaries, we have fought many battles, and we have been victorious," Splinter said. "But, do we know why?"
"Because shell we're good," Mikey answered, holding up his arm. Splinter smacked him with is staff. "Uh, sorry sensei."
Splinter cleared his throat. "We have survived these many trials and tests by following the path of ninjitsu and by finding and using?" Leo thought for a minute.
"Our inner strength?" he guessed.
"Yes, Leonardo, only by focusing on our inner strength can we overcome our enemies," Splinter finished. However, Mikey wasn't listening as he directed his attention towards the pool, confused. "Michelangelo, where is your focus?"
"Uh, right over there, sensei," he answered, pointing to the pool. Strange devices were floating in it. "In the pool."
"What the shell are those things?" Donnie questioned.
"Ground Force to Night Sky, the packages have been delivered," one of the drivers reported.
"Roger, Ground Force. Stand by."
Bishop stepped forward. "Proceed," he replied. The devices activated as they emitted a high frequency throughout the sewers. It drives the rats out, sending them running out into the streets. Leatherhead was hearing the frequencies as well.
"What is that noise?" he asked, painfully as he tried to cover his ears. "I can't think! It has to stop! Someone make it stop!"
In the lair, Splinter was having the same reaction as the rats, as well as Alopex. They both tried to cover their ears.
"Master Splinter?" Leo asked in concern and turned to Donnie. "Don, what's the matter with him?"
He picks up one of the devices. "It's these!"
"The sound, I can't block it out!" Splinter explained, painfully. He faints and Leo catches him in time.
"We need to get them out of here, now!" Leo shouted.
Everyone took the elevator up to the surface and climbed into the Battle Shell, driving off. On the streets, they still heard the sound coming from the devices as they were scattered throughout the city.
"Man, I'm hearing it up here, too!" Raph complained as he drove.
"There seems to be some kind of sonic disruption throughout the city," Donnie explained, looking out the window. "And although it doesn't appear to bother humans, it's clearly targeting to other species."
"Like rats," Leo replied.
"And foxes," Mikey added.
Bishop was in a helicopter. "Beginning sweep to mobile mutated genetic signatures," a soldier reported as he searched the screen until it spotted the Battle Shell. "Right there, sir. Looks like our target."
"Intercept them." Bishop ordered.
"Night Sky to Ground Force, Operation Mousetrap is a go. I repeat, Mousetrap is go."
Suddenly, vans swarmed in front of the oncoming Battle Shell, blocking the road. "What the shell?!" Raph exclaimed and quickly turned as they opened fire. He dodges the bullets, but helicopters were now hovering above, following. They launch several missiles at the Battle Shell.
"We got missiles incoming!" Mikey yelled as he looked out from the passenger side window. Raph manages to dodge some of the missiles but one manages to hit as it lands directly into the Battle Shell. Everyone screamed in surprise until the missile breaks apart, revealing small rounded beads inside of it.
"What are those things?" Mikey panicked.
"I don't know!" Donnie exclaimed. The beads unleash a strange gas and one by one it began knocking everyone out. The truck screeched to a stop as the turtles and girls, along with Mona, holding Elizabeth, tried to get out quickly but was succumbed by the gas, passing out on the street. Three black vans pulled up. Soldiers ran out and took Splinter and Elizabeth. They carried them into the vans and drove away, while several soldiers stayed behind to guard the turtles and girls.
"Targets acquired, sir."
"What about the turtles and girls?" Bishop asked on the other end of the radio.
"Neutralized, sir. Your orders?"
"No survivors," Bishop ordered. The soldier nods to the other three remaining men and they lifted their guns, aiming at the turtles and girls.
"You heard the man, let's finish this," the soldier ordered. Just as they were about to fire, a large shadow lunged out at the soldiers, attacking them. It was Leatherhead. Sounds of their screams haunted the streets before they went deadly silent.
The turtles and girls began to wake up as they found themselves in the abandoned train station. Leo noticed that Splinter was not there.
"Master Splinter!?"
Mona's eyes widen in horror realizing that Elizabeth was gone as well.
"No! Raph, Lizzie's gone!" she cried.
"What?!" Raph's eyes widen as he held Mona, trying to calm her down, and looked around. She wasn't there.
"They abducted them," Leatherhead explained. "I'm sorry, I couldn't stop them. Luckily, the gas was non-lethal."
"Which means, that whoever abducted your sensei and the little one, wanted them alive." a voice called out, surprising Leo and Leatherhead. The Fugitoid stepped out, walking towards everyone, his body was composed of salvaged parts.
"Whoa, new threads, Professor Honeycutt?" Mikey asked.
"Yes, those segments of my memory were purged. We recovered blueprints for my former Sal 1000 body. Overusing Earth technology makes it seem rather...homemade." he replied.
"I hope Master Splinter and Elizabeth are alright," Leo murmured, worried.
"Well, at least we know who took 'em. Those were Bishop's flunky commandos. Now, all we have to do is find 'em!" Raph growled.
"But how?" Donnie questioned.
"Wait a minute, we still have Bishop's subway train car, at least half of it,"
"Let's take this thing apart and find some answers," Leo said as they stepped into the car, starting to take it apart. Donnie placed his laptop next to the Fugitoid.
"I can't seem to hack into the system. A lot of this seems to be Federation and Triceraton tech."
"As well as other alien technology that I am unable to classify," the Fugitoid said. "Your Agent Bishop gets around for an Earthling."
"I don't think that he is even human to begin with," Yuuki commented.
"Wait, there," Leatherhead pointed to a blinking icon on the map. "An automatic recall layered into the train car sub circuitry."
"Hmm," the Fugitoid pondered. "If we reactivate it..."
"The recall signal should be triggered." Leatherhead finished.
"And if we're on board, it'll take us right to Bishop's location." Donnie added.
In Bishop's lab, Splinter was strapped to a gurney as he was starting to wake up. He struggled to break free out of his restraints.
"Oh good, you're awake, Master Splinter." Bishop said, walking up to him, holding Elizabeth.
"Bishop," Splinter glared at him. "Let the child go. She will be of no use to you."
"How wrong you are," the agent smirked, as he tickled Elizabeth's chin who responded back by trying to bite his finger. "Your unique genetic makeup has been very useful to me indeed as well as hers. In fact, the mutated DNA I'm extracting from you even as we speak will help save all humanity."
Splinter narrowed his eyes at him, gritting his teeth. "But, you look confused. Allow me to explain. I work for the Earth Protection Force, a secret government organization assembled to face a mounting crisis. A crisis dating back to 1870, when President Grant created the EPF."
A screen appeared behind Bishop as it came on, revealing a man that resembled Bishop standing next to the president. "After the first extraterrestrials crashed on Earth, extraterrestrials as crisis that continue to this day as we've seen with the recent invasion of those savage Triceratons." he turned to Splinter. "I guarantee you, similar invasions will follow. And someone has to be there to stop them. That is the purpose of the EPF, my purpose, to create a new humanity, a new superior race born of enhanced DNA."
Splinter saw that Bishop was hovering over something, lying on the table. "DNA that have been acquired from genetic manipulation, alien autopsies, and even stolen from your sons and the girls."
Splinter glared at him. "But, it was your mutated rat DNA being nearly so human that has allowed me to finally complete the process, and for that, I thank you." Bishop powered up his laboratory equipment. Electricity began to surge as it began to shock the specimen strapped on the table.
"Yes! It lives! The new evolution of humankind!" Splinter saw a person that looked like a human but it was wearing a helmet on their head and armor.
"The Slayer!"
The turtles and the girls, the Fugitoid and Leatherhead were riding on the train as it took them to the tracking location of Bishop's base.
"Okay," Raph called out, turning to them. "Next stop, Bishop Central."
Bishop walked past his experiments that were in glass tubes. "Not only are these future members of the Earth Protection Force, but they are the new humanity. These clones are awaiting the final DNA sequencing. By cellular acceleration, I can give birth to an army within six hours, fully trained thanks to my advances and bio-data transference. And your DNA. I've uploaded complex survival tactics into this prototype."
"What will you do with them?" Splinter asked, as a crane was lifting him up into the air.
"Mainstream them into the population, of course," Bishop answered. "We have aliens out there right now, living amongst us. My Slayers will ferret them all out."
"Lots of innocent people get "ferreted out." What if errors are made?" Splinter protested. The crane stopped as he was hovering over a glass container.
"Not my concern," Bishop replied. "I'm a bigger picture kind of guy. Besides, my calculations suggests that it would be beneficial if fifty-seven of the the Earth's population simply...disappeared." The crane lowered Splinter into the container. "Just think, my little lab rat. Your DNA will make it all possible. You're lucky you're such an unique organic specimen. You shall be preserved." The container was now beginning to fill up with a green liquid.
One of the soldiers, walked up to Bishop. "Sir, the recall signal for A13 has been activated," he reported. "It's on it's way in."
"Hmm," Bishop murmured, in thought. "That train should haven been destroyed. Prepare a suitable reception, just in case it's occupied."
The train approached as it rolled into a stop. The soldiers ran up to it, surrounding the train. A couple soldiers walked up to the car door. Leatherhead immediately attacked them. Donnie spinned his staff and kneed a soldier in the stomach. Donna jumped over a soldier, landing behind them, as they tried to attack her with their gun. She quickly turned around and slapped a glyph on their backs.
"Huh?" the guard asked confused. Donna smirked. The glyph activated as the guard was launched from off of his feet, slamming into the ceiling then flew at a couple of other soldiers, smacking into them. They fell off the edge, landing right on the train tracks. They let out a loud shriek as the tracks shocked them before going silent. Donnie and Venus both cringed as they watched with a shocked and disturbed look on their faces. Donna turned to them with a smile on her face.
"I'm sure they're okay," she reassured them, as she rubbed the back of her head. No, I'm pretty sure, in fact, that they're dead. Mikey runs up to two soldiers, who were firing at him. Leo and Yuuki disarmed them. "Leatherhead, the door!"
Leatherhead holds it up. "Hurry!" The Fugitoid, the turtles and the girls run over to him. "Hurry, I can't hold it much longer!" He holds it open for them as they run inside then drops it behind them. More guards ran over to the mutant gator.
"Alright, freak, slowly get to your feet and make no sudden moves," one of them orders. Leatherhead's eyes turned into slits, getting angry. He growls and turns around and attacks them.
The group quickly rush into Bishop's lab. They stop when they see Splinter in the containment tube.
"Master Splinter, no!" Leo cried out.
"Master Splinter!" Raph shouted. Everyone heard the sound of clapping to see Bishop as he approached them.
"Elizabeth!" Mona cried out as she saw her in Bishop's hands. Elizabeth's eyes widen happily as she saw Mona and Raph who had scared and angry looks on their faces. She tried to reach out to them with her hands.
"Baba! Mama!" she squealed, happily. Mona's and Raph's eyes widen in shock as well as everyone else's. Elizabeth had said her first words.
"Bishop!" Raph growled.
"I must say, I'm impressed that you found me," he smirked evilly as he told them. "but you won't be staying."
Everyone rushed towards him, but Bishop made no move as they got closer. Then the Slayer landed down in front of the agent, protecting him from everyone. Leo stepped back before charging at him. He tried to slice the Slayer with his swords but he dodges. The Slayer jumps over to the staircase as Leo tries to chase after Slayer turns around and kicks Leo away. Raph growls and charges towards him with his sais. But, the Slayer was quicker as he grabs onto the railing of the staircase and swings around and kicks Raph back.
Mikey ran up to him, spinning his nunchucks but the Slayer grabs them. He throws Mikey into the wall. Donnie jumps up, using his staff but the Slayer moves out of the way. Donnie swings his staff, but the Slayer dodges it and knocks Donnie down the stairs.
The Fugitoid inches over towards Leo as he gets up. "Get Master Splinter out of there!" he told the Fugitoid.
"Absolutely," the Fugitoid rans off, to where Master Splinter was as Leo lunged at the Slayer.
"I'll help." Donna pitched in, running off to help the Fugitoid.
Raph stabs his sai into the Slayer's arm, he flips over him. The Slayer pulls Raph's weapon out and the wound begins to heal by itself. Raph makes a shocked look as the armor breaks off from the Slayer's arm. The Slayer looks at it for a minute then grabs Raph's other sai, spinning them in his hands. Raph pushes Mikey out of the way as he throws his sais at them, stabbing a control panel. It sparks behind Raph as it exploded, knocking Raph to the ground. Leo ran on the catwalk above while Mikey and Alopex fought with the Slayer. Leo swings in on the crane, hitting the Slayer with his swords. He stumbles back, sparking. He pulls off his helmet, revealing his face. He had Bishop's face, but the other half was robotic as well.
Everyone gasped in shock. "Bishop?!" Donnie asked in surprise. Bishop's clone turned to them.
Bishop walked up to him. "Handsome devil, if I do say myself."
"Okay, now I'm officially freaked out!" Mikey commented while the others had their mouths still open in shock. The Slayer began to jump around, quickly.
"Oh believe me, you ain't seen nothing yet," Bishop added as the Slayer climbed on some tubes then turned his head, looking at everyone, without moving his whole body, then turned invisible.
"This just keeps getting better and better," Raph retorted, getting his sais. The Fugitoid and Donna walked up to the computer to free Splinter from the tube.
"Don't worry, Master Splinter," he assured. "I'll have you out of that nasty bio-suspension fluid in a jiffy." The crane moves and begins to lift Splinter out of the container. Suddenly, a chain with a claw hook latched onto the Fugitoid's arm.
"Oh dear," Bishop pulls the chain, ripping off the robot's arm. "That was totally uncalled for." Bishop throws the Fugitoid's arm away.
"Step away from those controls, cyborg."
Donna rushed towards Bishop as she tried to grab Elizabeth but he dodged her stepping to the side. Donna slammed a glyph down and an ice pillar shot out, catching Bishop off guard, making him accidentally let go of Elizabeth. Donna quickly rolled and caught her in time before she hit the floor.
"That was a close one," she sighed in relief. Elizabeth babbled as she cooed as she reached out squishing Donna's face with her hands.
"Not close enough," Bishop called out as he flipped over the ice pillar, landing behind Donna. Donna's eyes widen as she tried to cover Elizabeth in her arms. Bishop reached out to grab Elizabeth but Donna quickly ducked out of the way. She tried to run but Bishop grabbed her arm, pulling her back, hard. A loud snap was heard as Donna's arm was pulled out of it's socket and she yelled out in pain. She kicked Bishop back and flipped away from him, landing on her feet, still clutching Elizabeth in her other hand, tightly.
Then, the crane that was holding Splinter, drops him and it also breaks the gurney that he was strapped to, as it lands on the floor, freeing him. He was still soaking wet, as he faced Bishop.
"Bishop, you will not succeed!" Splinter shouted, as he picked up a pipe, spinning it.
"Wrong," Bishop corrected him. "Neither you nor your little green brats can stop me."
Raph and Donnie were with each other as they searched for the Slayer as well as everyone else who were in pairs. Suddenly, Slayer appears in front of Mikey and grabs him as he kicks Alopex away. "Guys, he's over hereee!" the Slayer throws him into the wall and flips, kicking Mikey against it. He falls to the floor and rubs his head as the Slayer escapes. "This guy doesn't play nice!"
"You don't understand," Bishop throws his hook at Splinter. "I've created life!" Splinter jumps over it and knocks Bishop down, pinning him with his pipe. Bishop flips, knocking Splinter off of him.
"Bishop, no one has the right to play God!" Splinter exclaimed. Bishop surprises Splinter as he pulled the chain using his hook to wrap around Splinter.
"I am taking the necessary steps to defend the world! It is my duty!" He breaks Splinter's pipe using the hook and flips Splinter over. Splinter lands on his feet.
"The world has enough monsters! It does not need yours!"
Raph and Mona were searching for the Slayer. He turns himself visible as he lands on a containment pod behind them. He jumped away, when Raph turned around, sensing him, while Mona continued on ahead. "Come out, come out wherever you are, you ugly freak." The Slayer appeared behind Raph and Raph turns around, growling. The Slayer turned invisible again and flips over Raph, kicking him from behind. Raph tried to charge at him but the Slayer grabs Raph's wrist and twists it. He slams Raph's sai into a pipe, pinning him to the wall as he punched Raph's shell repeatedly. Raph turned around and runs towards the Slayer only for him to grab Raph and lift him up and toss him to the ground.
Not to far off, Leo and Yuuki heard fighting in the distance.
"Raph?" Leo murmured and gasped, before turning to Yuuki.
"Let's hurry!" she quickly told him. They quickly turned around the corner, only for Raph to be shot out in front of them, as he was thrown, crashing into some of the pods nearby, where Mona was. A containment pod falls on top of Raph, as he struggles to hold it up, and sees another one of Bishop's clones inside of it.
"Bishop?"
Leo and Yuuki jump, down hearing a growl. They looked up to see the Slayer climbing on the vent and saw that he was heading towards Splinter. They followed after it. Splinter kicks Bishop from behind as the Slayer jumps down, getting ready to attack Splinter. Leo and Yuuki jumped into the air and kicked him. The Slayer lands into the containment tube with the liquid.
"Professor Honeycutt, the tank! Seal it!" Leo shouted.
The Fugitoid sends an electric current into the vat, shocking the Slayer as well. Bishop gets up to see what is happening. "No! My Slayer!" Splinter jumps up and kicks him.
"This is over, Bishop!"
Bishop adjusted his glasses and turned to see Splinter charging at him. He jumps and lands on the hook, hanging from the ceiling.
"My plans are far from over, rodent!" Bishop jumps off from it and lands. "You have no idea!" He grabs his chain, spinning it. Splinter glared at him and Bishop throws the chain at him. Splinter uses his pipe to block it but Bishop takes it from him. Splinter jumps over a gurney and Bishop breaks a part of it with his chain. He throws the gurney at a shocked Splinter. Splinter kicked it, breaking it into pieces. Bishop throws his chain and the hook latches onto a engine turbine.
Splinter bends down and picks up a piece of the gurney and throws it at a lever, activating the machine. Electricity from the turbine shocks Bishop, electrocuting him. He growls and pulls the chain off, but the turbine explodes. Bishop and Splinter are sent flying in different directions from the explosion. Bishop was impaled by a hook on a chain, screaming.
Raph and Mona rushed over to Donna, as did everyone else, as she handed Elizabeth over to Mona.
"Elizabeth!" Mona shouted as she took her from Donna.
"Whoa, dudette, your arm!" Mikey shouted in concern. Donna hissed in pain as she tried to support her arm. Venus used her chi magic to try to lessen the pain on Donna's dislocated shoulder.
"I'll pop it back into place," Donnie told her as he was about to. But, Donna moved his hand away.
"There's no time," she told them. "We need to find Splinter."
Splinter groaned as he got up, seeing Bishop on the hook, but also saw that the explosion had caused fires, too.
"Sensei!" He turned to see everyone running towards him.
"My children," he said in relief.
"We have to get out of here!" Leo told him. The fire and the explosion had caused water to start flooding the room as well. Splinter looked back towards Bishop to find him not there. He was gone!
"You will pay for this, mutants," everyone gasped as they saw him climbing up a ladder, escaping. "One day, you will all pay!" They all ran over to the ladder, following him.
"After him!" Mikey yelled as Splinter climbed up it first. More turbines exploded as the room was beginning to flood, destroying the lab. The flood water also carried the Slayer's tube, as it fell down a pipe, just as the lab was destroyed. Everyone soon found themselves in an elevator as it carried them up to the streets and ran out of it, water rushing out of it as they did.
"Whoa, we're in the middle of Midtown!" Mikey said. They didn't see Bishop anywhere. He had somehow managed to elude them.
"And Bishop's nowhere in sight." Leo pointed out.
"We will see him again. Such men are hard to destroy." Splinter told them.