Down in the lair, Donny was going over every last piece of tech off the Foot-Tech ninjas suits. They were still covered in extinguisher foam, the purple turtle too preoccupied with dismantling them to clean them.

"This is some serious heavy duty hardware." He admitted. "Whoever built this is almost as smart as I am."

"So is there any way to find who made it?" Leo asked.

"I'm not sure, I-" Donny answered before something caught his eye. "Well now. What do we have here?"

"What is it?" Mikey asked.

"It looks like someone built some kind of monitor system into the eyes of the mask." Donny explained. "In fact, it looks similar to the type that was on Leatherhead's collar."

Hisako sat up straight when he said that, going stock still.

"What?" she asked, her voice almost a dead whisper.

Donny looked over at Hisako, mentally kicking himself.

"I uh... I examined the tech in that collar you pulled off Leatherhead back when we first met him." he explained sheepishly. "I was curious and... and this tech is almost identical to that."

Hisako started breathing heavily, going a bit pale as she curled up into a ball. Raph glared at Donny, whacking him upside the head.

"Way to go, Don." he chastised. "You freaked her out!"

"Sorry." Donny apologized. "It's just... I can only think of one person who could make this kind of tech, and he's supposed to be an amnesiac."

"That guy is gone, Donny." Leo told him. "He's gone and he's never coming back!"

Hisako was rocking back and forth on the couch, trying to keep herself calm. Splinter saw this as he walked out of his room and went over to comfort her.

"It is alright, Hisako." He reassured, wrapping his arms around her. "You are safe here."

She was still breathing hard, old fears rising to the surface. She clung to Splinter's robe desperately, shivering violently.

"Think I should call LH?" Mikey asked.

"Might be a good idea." Leo agreed.

Mikey took out his shell cell and called Leatherhead. The croc picked up almost immediately, much to the orange turtle's relief.

"Hey Leatherhead." Mikey spoke. "Listen, Hisako needs some comfort right now. How fast do you think you can-?"

The line went dead before he could finish his question.

"Hey Hisako, Leatherhead will be here soon!" Mikey called out.

She didn't reply, remaining in Splinter's arms as the rat attempted to comfort her.

"Just to be safe," Leo whispered to Raph. "Maybe someone should check on the state of 'you know who'."

"I'll call Casey and see if he's willing to pop by." Raph whispered back. "Besides, if anything, we could use some extra hands on deck once Donny locates the wackbag behind all this."

"Sounds good." Leo replied.

...

On board Shredder's ship, Shredder had finished putting on his armor, testing it to make sure it had not gotten damaged after his last battle. There were several training dummies set up and he wasted no time slashing through all of them. He allowed a smirk to grace his face as the blades proved just as sharp and deadly as ever.

"I hope your armor is up to your specifications, Master." Hun announced, bowing before his master.

"It is, Hun." Shredder confirmed. "The next time I face Hamato Yoshi and his infernal followers, I will not fail."

...

The door to the lair shook under the weight of a heavy hand pounding on it mercilessly. Mikey quickly slid over to the door, opening it to reveal Leatherhead.

"Glad you made it." Mikey told him. "Hisako's over-"

LH pushed right past him, making his way over to the couch. Master Splinter carefully moved out of the way as the large crocodile picked up Hisako.

"Oracle..." he said softly, caressing her face gently.

She curled up in his grip as he held her tightly, noting just how scared she was.

"What... happened?" the croc questioned.

"Someone sent invisible ninjas after us." Raph explained. "They had some... familiar tech attached to them."

"Familiar how?" LH demanded.

Leo, Raph, and Mikey all looked over at Don, allowing him the 'pleasure' of explaining.

"The tech in their suits was similar to..." He explained. "The collar you were wearing when you first attacked us."

Leatherhead went stiff, his eyes glowing red slightly as his grip on Hisako tightened.

"How... is that... possible?" he snarled, barely containing his rage.

"We don't know!" Donny quickly answered. "We're looking into it now."

About that time, the elevator into dinged as Casey made his way inside. He had his equipment bag over his shoulder, and his hockey mask in his hand.

"Yo guys." he called out, taking stock of the scene. "Yikes. If Leatherhead's here, things must be pretty bad."

"Yeah." Raph confirmed. "What'd you find out?"

"Well, I got good news for Greeny and LH." Casey declared. "That sadistic wackbag is still memoryless and locked up in the asylum. You got nothing to worry about."

Leatherhead visibly relaxed, the glow fading from his eyes. Hisako did the same, sagging in LH's grip.

"Thank shell..." she whispered.

"Well if he didn't make it, who did?" Mikey asked.

"We may find out soon enough." Donny answered. "If they were broadcasting footage, I might be able to track the signal."

"Then get tracking Donny." Leo told him. "The sooner we take down whoever's behind this, the better."

Donny nodded, then got to work tracing the signal back. On his computer, a map of New York popped up onto the screen. It slowly began zooming in, focusing in on the harbor.

"Got em!" He let out. "Looks like they're stationed at the harbor. Probably on some kind of freighter if I had to guess."

"Then what the shell are we waiting for?" Raph asked. "Let's go bust some heads!"

"I'm coming with you." Casey declared, sliding his mask onto his head. "If you guys don't mind sharing the action."

"Not at all." Raph replied.

"I will go as well." Splinter spoke up. "If there are those that wish to continue Saki's work, then they must be stopped."

"I'm... coming... too." LH declared, sliding Hisako onto his back. "Someone has... his tech..."

"Say no more, big guy." Mikey replied. "Let's move!"

Leo turned to him in annoyance. Mikey saw this and chuckled nervously.

"Ok... you say it." Mikey told him.

"Let's move." Leo declared.

...

Sometime later, the turtles, Hisako, Miwa, Splinter, Casey, and Leatherhead arrived at the New York Shipping yard. They kept low and hidden behind a crate, peering out at the ships. Donny peeked out from behind the crate and took a look at his shell cell, seeing that it was pointing him to a freighter with a Foot logo on it.

"There it is." He told them. "The source of the signal."

"That's the Shen, The Shredder's personal vessel." Miwa explained.

"He named it after the girl who dumped him?" Mikey asked. "Man, he was obsessed."

"We need to get inside and see what we're up against." Leo declared.

"To do that, we need to be stealthy." Donnie reported. "Unfortunately, that leaves Leatherhead out."

"Hisako too, just in case." Leo agreed. "We can't risk her having a panic attack and giving away our location."

"Sounds good." Leo agreed. "Mikey, you stay and keep an eye on her just in case. Don.... you stay and watch Mikey."

"Hey!" Mikey let out.

Leaving LH, Hisako, Don, and Mikey on the pier, Leo, Raph, Miwa, and Splinter slunk towards the ship. Raph jumped on one of the ropes and climbed up onto the ship. Once he got up there, he saw a Motorhead walking away from him. He quickly grabbed him and put him in a choke hold, knocking him unconscious. Another Motorhead turned around and tried to intervene, but was quickly brought down by Miwa. A third Motorhead backed away towards the ramp, but Splinter quickly swept his legs out from under him before bringing his stick down on his stomach, taking him out. Leo quickly came up and threw another Motorhead off the ship, sending him plunging into the drink.

"That takes care of them." Leo remarked. "Now to get inside."

"Got that covered." Raph reassured, walking over to a nearby air vent and prying the grate off. One by one, they all piled into the vent, Miwa taking the lead with Splinter right behind her. Raph went in first as Leo took up the rear, pulling the vent back in place to cover their tracks. They crawled further and further into the ship, finally coming across a nearby vent. They looked inside and saw a large lab that looked all too familiar to the turtles and Splinter

"Holy Chalupa..." Raph let out.

"It's another TCRI." Leo whispered.

"Perhaps leaving your sister on the docks was a wise course of action." Splinter declared.

"Yeah, but without 'you know who', how did they get this place up and running?" Raph asked.

"They must have someone new working on this." Leo deduced. "Miwa, did Shredder have any other scientists working for him?"

"Not that I- wait." she realized. "There was this new doctor he hired not long before I defected. His name was Dr. Chaplain. I thought he was just a medical doctor, but he may have been Shredder's new scientific officer."

"Then he's cooking up this crap?" Raph asked.

"It matters little." Splinter replied. "The mere presence of this facility is a danger to us and this city. It must be completely and totally destroyed."

"Right." Leo agreed, pulling out his shell cell. "Guys, you there?"

...

Donny pulled out his shell cell, putting it on speaker.

"You're life, Leo." he announced. "What's going on?"

"We need to blow the ship." Leo told them. "First we need to get it out to open waters, away from the city. Hisako, you, Mikey, and Leatherhead cut the mooring lines tying us to the dock. Raph, Miwa, Splinter, and I will head to the bridge and get this puppy moving. Donny, think you and Casey can sink this thing?

"Sinking a two ton freighter sitting on a mountain of diesel fuel?" Donny remarked. "Sounds like a walk in the park."

"Always wanted to blow something up." Casey commented, sliding his mask over his face. "Let's do this."

With that, Donny and Casey ran towards the ship. Hisako looked down at LH with a smirk, one she shared with Mikey.

"Well, you heard Leo." she declared. "We've got mooring lines to sever."

"Let's roll." Mikey declared.

...

Meanwhile in the captain's quarters, Shredder watched several monitors. He noticed the men Splinter, Leo, Raph, and Miwa had managed to take down, and he also saw a blur of purple making its way towards the engine room.

"Our guests have arrived." he declared before turning to address the rest of the room's occupants. "Elites, go down into the engine room and welcome our intruder. Hun, you and I will see to Yoshi and his children personally."

"Master, what makes you think the rat is here?"

"I just know, Yoshi won't miss the chance to clash with me again." Shredder remarked.

...

In the bridge, the Hamato clan emerged from the ventilation shaft, straightening up and looking around.

"Coast is clear." Miwa declared. "Don't know how long that will last though."

"Then let's work fast." Leo told them.

Raph made it to the control panel and looked over the controls.

"Yeesh, all these buttons and not one of them says 'on'." Raph remarked.

As they kept working at it, the door to the control bridge swung open, revealing Hun in all his muscled glory.

"Good evening." He declared. "I'm afraid you're all trespassing, and the Captain doesn't take lightly to stowaways."

"Well, well," Raph remarked, drawing his sai. "If it ain't our favorite wall of muscle."

"No way you're the captain of this operation, Hun." Miwa snapped. "You barely have two brain cells to rub together."

"He isn't," Shredder's voice replied. "But I am."

The four of them turned around to see Shredder walking out of the shadows towards them. Miwa's eyes went wide, stumbling back in fear. Leo and Raph both stared, their mouths agape in horror. Splinter shook in shock and anger, gripping his walking stick tightly.

"Saki..." he whispered. "How is this possible?!"

"I found a way to survive before." Shredder told him. "As I did from our last encounter. Though it seems I am not the only one too stubborn to die."

Splinter stepped forward, holding his stick up in a defensive stance.

"I will never fall to the likes of you, Saki." he declared defiantly. "You will pay for everything you have done! To this city, to my family, to my daughter!"

"We shall see, 'old friend'." Shredder retorted, readying his claws. "Hun, kill them!"

Hun quickly punched Raph, knocking him into a wall. Leo leapt at him, trying to kick him in the face. Hun quickly grabbed Leo's leg and threw him at Raph. Splinter wasted no time charging at Shredder, clashing his stick against his claws. Shredder shoved him off, trying to slash at him. Splinter quickly blocked the strike with his stick and tried swinging it at Shredder. He quickly dodged the attack, countering with a swift kick to the gut. Splinter tumbled back, and Miwa stepped forward, her katana raised.

"I won't let you hurt my father again!" she shouted, bringing her sword down on Shredder.

"Then our time together has truly meant nothing to you." Shredder remarked, shoving Miwa away.

"You're wrong." she told him. "I can't erase what you did to me. The seventeen years of lies! And deceit! And hatred!"

Miwa then continued slashing at Shredder, with him dodging and blocking every strike.

"You stole me from my true family!" she cried. "You raised me to hate the man that was truly my father! I was nothing more than another tool for your revenge!"

She then kicked him in the chest, sending him skidding back. She ran towards him ready to stab him, but he quickly caught the blade in his claw.

"You should have been mine from the beginning." Shredder told her. "You were always supposed to be my child! That is why I raised you, trained you! You never went without, nothing was forbidden to you! You would throw all that away for living with freaks in a sewer, Karai?!"

"In a heartbeat!" she declared. "And my name! Is! MIWA!!"

Enraged, Shredder snapped the blade with his claw and threw her against the wall.

"This has gone far enough!" Shredder yelled.

"On that, we agree!" Splinter replied, running towards him and tackling him to the ground.

...

In the engine room, Casey and Donny were hunched over the main engine of the ship, both of them analyzing it with strategic eyes.

"Man, I don't think we're gonna have enough diesel fuel to take down this rig." Casey pointed out.

"I thought about that." Donny informed him. "This ship has stores of mutagen onboard, and we've learned that it's highly combustible."

"So we grab some mutagen, haul it down here, and blow this place to kingdom come." Casey decided.

"Exactly." Donny replied. "I think six outta do it."

"Then we best get to hauling." Casey announced.

Before they could move though, a large cloud of smoke appeared in front of them, revealing the five Foot Elites barring their way.

"Uh-oh, these guys." Casey swore, grabbing his baseball bat from his bag.

"I don't suppose you five would be willing to help us out." Donny tried, readying his staff.

The elites brandished their weapons and charged at them. Donny blocked the spear elite's weapon and knocked him back. Casey knocked the legs out from under one, hitting him hard enough in the head to knock him out. Donny saw a nearby steam pipe and broke it with his staff. Steam filled the room and Donny and Casey used the cover to take out the remaining elites. When the steam cleared, Donny and Casey stood over their unconscious foes triumphant.

"Too bad." Casey lamented. "The extra hands would have been helpful."

"Come on." Donny told him. "We have work to do."

...

Back outside, Leatherhead tore out one of the moorings from the dock with no problem. Hisako was on his shoulders, dislodging another one with her telekinesis. Mikey untied another one of the ropes.

"I think that's the last of them." he announced. "We need to get up there."

Hisako looked wearily up at the ship, cringing a bit at the idea. Leatherhead patted her leg gently, trying to help her calm down.

"Ok... new idea." Mikey decided. "I'll go. You guys can stay here."

Mikey then leapt onto one of the ropes and climbed up it, leaving Hisako and Leatherhead on the dock, watching the orange turtle disappear onto the deck.

"Oracle..." LH let out. "Your family... needs you..."

She gulps, then steels herself.

"Right." she told him. "Think you can make that-"

Leatherhead launched himself onto one of the ropes, grabbing onto it as quickly as he could. They swayed slightly, but soon stabilized.

"-jump." she concluded.

Leatherhead then climbed up the ropes towards the deck of the ship.

...

Back in the bridge, while Splinter and Shredder continued to clash, Raph and Leo resumed their battle with Hun. Raph ran up and kept punching him in the gut, but Hun just backhanded him. Leo came up and kicked Hun in the back of the leg, causing him to bend over. A thin, silver chain with a small medallion slid out of his shirt, one that Raph took advantage of.

"Nice jewelry, Hun." he quipped before grabbing the chain and using it to try and choke the behemoth. "Let's see how durable it is!"

Hun began to cough and wheeze, clawing at the chain to try and loosen it. The chain itself seemed to stretch, revealing some thin wires hidden in the metal. They sparked and fizzed slightly, and for a split second, Hun seemed to change before their eyes. It may have been a trick of the light, but his skin had seemed a dark shade of green.

"Huh?" Raph let out "What the-"

Before Raph could finish, Hun managed to grab him from behind, tossing him over his shoulders and into a wall. He gasped for air, unaware that Leo was running up from behind him. As Hun turned around, Leo leapt into the air and sliced at him. Hun was barely able to dodge, but his chain was severed in the attack. Suddenly, his form began to change. His skin turned green, his teeth sharpened, and his chest transformed into a thick, light green shell.

"What. The. Shell?!" Raph let out.

"Hun's a- a-" Leo tried.

"The word you're looking for is Gamaron." Hun supplied, getting to his feet and grinning with his razor-sharp teeth.

"Did you know about this?" Leo asked Miwa.

Miwa shook her head in shock.

"No." she whispered. "No I did not."

"I supposed there's no use hiding it anymore, Hun." Shredder declared. "No need to hold back either."

"He's been holding back?!" Leo and Raph both exclaimed.

Hun responded by swatting both Raph and Leo aside, sending them slamming into a wall. Raph quickly got up and brandished both his sai as he charged at him. He tried slicing at Hun, but he blocked it with his claws. Hun then slashed at Raph, who quickly turned around so the slash would hit his shell. Even then, it still hurt a lot.

"Okay, if this is what a Gamaron can do, I'm kinda glad we didn't run into any when we were in space." Raph grunted.

"Tell me about it." Leo groaned.

Across the room, Splinter and Miwa continued to clash with Shredder. The bladed ninja was able to keep up and block the attacks of the father daughter team. However, once Hun began to turn the tide in his favor, Splinter's attention was divided.

"Go dad." Miwa insisted. "I can handle Shredder for a little bit."

"I will not leave you!" Splinter told her.

"How noble." Shredder remarked, blocking Splinter stick.

"Fine, then I'll go deal with Hun." she declared.

She slid away from Shredder, leaving Splinter to face him. She then ran up to Hun, jumping into the air with her sword raised. Hun easily grabbed her and threw her to the ground. She hit the floor hard, almost falling unconscious.

"Miwa!" Splinter let out.

Shredder took advantage of Splinter's distraction and swatted his stick away before grabbing his shoulders and kneeing him in the chest. He then threw him against the wall and moved towards him, impaling his claws inches from his head.

"Finally," Shredder let out in delight. "You are mine."

"No!" Miwa screamed. "Stop!"

Leo and Raph went to try and help their father, but Hun grabbed them both by the hair, holding them back with a grin of anticipation.

"Shredder!" Raph yelled. "If you harm one hair on Master Splinter's body, you're gonna wish you were never born!"

"From where I stand, you're not in a position to do anything." Shredder remarked, picking Splinter up by the robe and readying his claw. "And now, after nearly twenty years... it finally ends!"

"No, stop!" Miwa cried out, grabbing Shredder's arm in desperation. "Please, don't kill him!"

"Give me one reason why I should spare his wretched life." Shredder asked.

Miwa looked at Splinter, then back at Leo and Raph. She closed her eyes, took a deep breath, and then sank to her knees.

"Spare them... and I will come-" she choked slightly, but forced herself to continue. "-home."

"What?!" Raph and Leo let out.

"Miwa, no!" Splinter insisted.

"Silence!" Shredder told him. "Do you mean that?"

"I do." she promised. "Spare the Hamato clan, and I will come home to you. I will be your daughter again, just please... let them live."

Shredder pondered for a moment before finally tossing Splinter aside.

"Very well." Shredder allowed. "Having you back by my side will be worth tolerating this rat's existence."

Shredder then walked over to Miwa and held out his hand.

"Welcome home, my daughter."

"She's not your daughter!" Hisako's voice shouted out.

Everyone looked up just in time to see Leatherhead burst through the window. His eyes were bright red as he dropped both Hisako and Mikey, the two ninjas drawing their weapons.

"And you're not taking her anywhere!" Hisako promised.

"Who invited the walking handbag?" Hun remarked.

Leatherhead then charged at Hun. Hun dropped Raph and Leo, catching Leatherhead's arms with his own. As the two struggled for a bit, Leatherhead shoved him off and whipped him with his tail. As Hun collided with the wall, Leatherhead ran over and punched him in the face repeatedly, not giving him even a second to react. Hun then uppercutted Leatherhead, forcing him back. As Leatherhead tumbled back, Hun charged at him. Leatherhead then quickly picked Hun up and threw him out the window.

"Crud!!" Hun shouted as he fell into the water below.

Raph snorted, then turned to Shredder with a grin.

"Ain't so tough without your walking muscle, are ya?" he taunted.

Miwa grinned slapping Shredder's hand away and getting to her feet.

"Thanks for coming Hisako." she told her sister as she reclaimed her weapon.

"Anytime, Miwa." Hisako replied before turning to Shredder. "Sorry Shredder, you've lost."

Shredder growled in response as he turned towards the turtles and Hisako.

"You freaks seem to ruin every one of my plans!" Shredder let out. "Well no more!"

Shredder lunged at them, but Leatherhead intercepted him, tackling him to the ground. Shredder punched and slashed at Leatherhead, but the croc merely sank his jaw into Shredder's right arm. The bladed ninja howled in pain, something that was only made worse when Leatherhead wrenched his head to the side, completely severing Shredder's arm.

"Oh holy shell!" Raph exclaimed.

Mikey covered his mouth as he attempted to keep himself from barfing. Leo cringed at the sight. Splinter averted his eyes, covering Miwa's and Hisako's as he did.

...

Meanwhile, Donny and Casey got several barrels of mutagen set up in the engine room. After some creative rewiring on Donny's part, the ship was set to blow.

"Alright, how much time do we have?" Casey questioned.

"About five minutes." Donny answered. "Though sooner would be better."

"Right." Casey agreed. "Let's book!"

Donny nodded and the two of them bolted out of the engine room.

...

Leatherhead spat out the severed arm in disgust, then he released Shredder from his grip, causing him to drop to the floor as he clutched his massive wound. The Hamato clan gathered around him, all of them with their weapons drawn.

"It is over, Saki." Splinter told him. "End this, and we can see you get medical attention."

"I... will never surrender... To you..." Shredder told him.

"Uh, sir." Chaplin's voice sounded off through the intercoms. "We have a problem. Several barrels of mutagen are missing from the lab!"

"Donny?" Mikey questioned.

"Donny." Raph, Leo, Hisako and Miwa all answered in unison.

Shredder turned to them, slowly losing consciousness as he lost more and more blood.

"What... have you... done?" he snarled.

"If I had to guess, rig this whole ship to blow to kingdom come." Leo told him.

"Bingo, Leo!" Donny declared as he and Casey came running into the room. "Everyone off this ship!"

"Say no more, brochacho." Mikey replied as everyone took off.

Shredder gathered what strength he had left to get to his feet and walk out of the bridge, growing weaker with every step.

...

The Hamato Clan with Casey and Leatherhead in tow made their way onto the deck of the ship.

"No time for a lifeboat!" Casey shouted. "I hope everyone can swim!"

One by one, everyone vaulted over the edge of the ship, splashing down into the water. No sooner had they all started swimming for shore, the ship exploded with a mighty bang, causing large waves to ripple out that nearly swallowed them all. They recovered relatively quickly, surfacing and coughing up water before looking out at the burning wreckage of the ship.

"Whoa..." Casey let out, pushing his mask up onto the top of his head. "That was a lot bigger than I thought it would be."

"It got the job done." Donny told him. "That's all that matters."

"And we're alive." Mikey added. "That's pretty nice too."

"Do you think the Shredder survived?" Leo questioned.

"Leo, LH ripped his arm off." Raph reminded him. "If the blood loss didn't kill him, the explosion did."

"I still can't believe you did that LH." Hisako remarked. "Are you okay?"

LH just growled.

"I do not.... Wish... to discuss it..." he informed her.

"Fair enough." She replied.

"It is too soon to say whether Saki survived or not." Splinter told them. "For now, let us go home. To enjoy the peace we have earned here tonight."

"I gotta admit, home sounds pretty good right about now." Leo replied.

"Agreed." Miwa announced. "Let's go home."

They began swimming for shore, leaving the wreckage behind them.

"Just so we're clear, I'm bunking with you guys tonight." Casey declared. "Explaining this to my mom will be impossible."

...

Hun swam through the water as fast as he could, dragging the unconscious bodies of both Dr. Chaplain and Shredder behind him. The three of them washed up on the shores near a ship repair yard. Hun looked down at his fallen master, snarling at the bloody stump that was now Shredder's arm.

"Crud." he swore, looking around.

He found a welding torch stashed in a garage and grabbed it, turning it on to the lowest heat possible.

"Forgive me master." he begged before applying the torch to Shredder's stump.

Shredder cried out in pain as the flames closed up his wound. He opened his eyes as Hun put away the torch, removing his master's helmet.

"Master, you live." he said gratefully.

"Indeed..." Shredder replied, looking at where his arm once was. "Barely."

"The doctor can repair you." Hun informed him, kicking Chaplain.

"Were you able... to salvage... anything else?" Shredder asked.

"No." Hun answered. "But, all back-ups of the hard drive are still at the safe house, as is our remaining mutagen supply."

"The turtles' actions here... have changed things." Shredder decided. "I think it wise.... To accelerate our plans."

"Of course, Master." Hun agreed. "After you have healed, this city will bow before you."

"And Hamato Yoshi and his infernal freaks... will die." Shredder added.

Hun nodded, then gently scooped up Shredder in one arm. He then grabbed Dr. Chaplain by the collar of his coat, and then made his way away from the docks.