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This is a transcript for City at War, Part Three (2003 TV series), the sixteenth episode of season two of TMNT (2003 series).

VOICE-OVER INTRO
Raphael You know, lately, Leo's been real a pain in my shell. He's on this whole kick about how we're responsible for the fact that the entire city seems to be at war. The Purple Dragons, the mob, and the Foot Ninjas are all squabbling over the pieces of Shredder's empire now that he's gone and Leo says it's our fault 'cause we're the ones that knocked out the Shredder in the first place. And for some reason, he thinks we're responsible for a whole lot of innocent people getting caught in the crossfire. And just when the whole deal couldn't get any crazier, this new wild card shows up and actually manages to make things worse. The only good thing I can say about Leo right now is... when he picks a fight, he really picks a fight.

{Opening sequence; title song}

The episode begins where City at War, Part Two left off, with Karai standing over Leonardo and holding her tanto at his head.
Karai Drop your weapons! [Raphael growls and advances a few steps.] I said, drop your weapons.
She moves her tanto closer to Leonardo’s neck. Michelangelo, Donatello and Casey all drop their weapons. Raphael does not.
Donatello Uh, Raph, didn’t you hear the nice lady with the knife?
Leonardo Don’t do me any favors, Raph.
Raphael growls again and then flips his sai over to grab them by the tips. He flings them and they pierce the rooftop near Leonardo.
Karai Good. Perhaps now we can talk.
Donatello Oh, you wanna talk? ‘Cause I kinda got the idea that you wanted to kick our shells.
Karai If I had wanted to destroy you, you would not be alive to talk.
Leonardo Okay, let’s talk. But it’s going to be difficult with your tanto at my head.
Karai steps back and sheaths her weapon. Leonardo springs to his feet, but then Raphael charges, springs off of his hands to land near he sai and retrieves them. He then leaps at Kara, but before he can strike, Leonardo catches Raphael’s weapons on his katana.
Leonardo Raph, no! I gave her my word of honor!
Raphael Your honor? [They separate.] Bro’, you are really getting under my shell!
Casey Jones Come on, Raph. Let’s hear what the pretty ninja lady has to say.
Karai As I told you, my name is Karai. [Her aides kneel before her. The tall aide takes a medallion strung on a ribbon from his cloak and hands it to her. She displays the gold medallion, which is emblazoned with the Foot Clan symbol.] And I command the Foot Clan in Japan. I am here to restore order to the New York faction of The Foot. When you turtle men destroyed The Shredder, you threw the city into chaos. We in Japan had hoped all parties would destroy each other like a snake which consumes itself, leaving the city once again under The Foot’s control. But we did not expect the city to be consumed in the process. If the Foot is to regain control of its New York operations, I will need your help.
Raphael We done talking yet? Is it time to fight?
Karai You are impudent! If you were my retainer, I would have you beaten!
Raphael Oh, yeah, you’re Foot all right.  [He runs at her, but Donatello and Michelangelo grab hold of him and pull him back.] You even sound like The Shredder!
Donatello Lady, even if we wanted to, I don’t see how we could help you. This war’s out of control. We’re kinda in over our heads as it is.
Karai Yes, I know. But I have a plan to stop this war.
Leonardo Then why do you need us?
Karai All plans must have their... contingencies. Make your decision.
She moves away from them leaving Casey and the turtles to talk.
Leonardo Well, what do you think, guys?
Raphael I think she can swim her butt back to Japan.
Casey I think she’s perfect. Looks, brains, and she’s a ninja.
Michelangelo What does she mean by “contingencies”?
Leonardo She means we’re Plan B.
Donatello There seems to be one thing missing from this equation. Uh, excuse me. What’s in it for us?
Karai Three things. One, you can save New York from being torn apart. Two, you can free your streets of the Purple Dragons and the mob. [She approaches Leonardo.] And three, the Foot and the Foot Elite are honor-bound to slay the one who defeated their master. They shall be relentless. They will destroy you, your master and your comrades. But if you help us, there will be no revenge for The Shredder’s destruction.
She walks away again and the group huddles.
Leonardo Listen, this is the chance we’ve been looking for. We can set things right. It may be a deal with the devil, but at least it’s a devil we know. I say we play along for now.
Donatello The turtles team up with The Foot? It sounds crazy.
Michelangelo I don’t know, Leo.
Raphael Urgh, I’ve heard enough! There’s no way I’m teaming up with Little Miss Foot!
Leonardo Raph, listen to me! We all know this thing is too big for us to fix.
Raphael Listening to you is what got us into this mess in the first place!
Leonardo We have to take this opportunity!
Raphael Oh, is that the “honorable thing” to do? You guys can be the Foot’s little toes if you want. But not me. I’m outta here! You comin’, Case?
Casey You know, Raph, I was always taught that no matter what, you fix your mistakes. I’m staying.
Raphael Whatever!
He runs to the edge of the building and leaps off. Karai walks up to the remaining group.
Karai Well?
Leonardo We accept your offer of alliance.
Michelangelo But no funny stuff.
Donatello We’ve never had much reason to trust The Foot before.
Karai The Foot has never had to ask for aid before. Now let us begin. We haven’t much time. Listen closely.
The scene shifts from day to night. The Foot Elite are seen running the rooftops. They stop and look up to see, standing atop a tall building, what appears to be The Shredder. They gasp.
Twin-Blade Elite Master? [The Shredder laughs.] Master! You’re alive! But how?
Shredder That is of no importance! Follow me!
Battle Axe Elite Our master has returned.
The Shredder runs across rooftops, pausing to look back to see if his minions are following before continuing.  Shift to the panel truck belonging to the mob. It lays on its side, in ruins. Fists smash into the top from inside before the metal falls away and Baxter Stockman steps out.
Stockman I’m alive. Alive! Once again, I have made a fool of fate!
The mob boss walks out of the wreck as well.
Mob Boss I thought we were gonna sleep with the fishes for sure. Let’s get back into the fight. Uh-oh. [They find themselves face-to-face with Hun and the Purple Dragons.] How you doin’, boys?
Stockman Ah! Hun!
Mob Boss Don’t worry. I’ll make him an offer they can’t understand. Gentlemen--  Whoa.
He looks up to see The Shredder standing atop a building looking down at them.
Stockman Oh! The Shredder. I’m doomed! I’m doomed!
Hun Master.
Shredder I have work for you to do.
He turns to leave.
Hun Purple Dragons, follow me.
The Purple Dragons follow.
Stockman They’re leaving. We’re going to live. We’re going to live!
A pair of cars come racing around the corner, tires squealing. They brake to a stop in front of the Mob Boss and Stockman. Weasel steps out of the front car.
Mob Boss Weasel, the Shredder’s back. [He gets into the car.] Seems the guy doesn’t know when to stay in the morgue. We are gonna own this city no matter what. Let’s just see if we can put that guy down for good.
They drive off. Shredder continues leading the Foot and the Purple Dragons across rooftops and through the streets. The Shredder enters the rooftop dojo of the partially destroyed Foot Headquarters building. There, Casey and three of the turtles are waiting.
Donatello So?
Shredder Ha! They have all taken my bait and are following me here. They shall arrive within minutes. They are in... [The helmet is removed to reveal Karai.] for a surprise.
Donatello Nice voice synth technology. You sound just like the Shredder.
Michelangelo Hearing the Shredder’s voice gives me the shivers.
Leonardo I don’t understand how you can serve someone as evil and dishonorable as the Shredder.
Karai You knew the Shredder only as a merciless enemy. But I knew another side of him.
Flashback to years earlier in Japan. The Shredder walks through the rain, carrying an umbrella.
Karai It was he who discovered me many years ago in Japan, after my parents had abandoned me. [The Shredder stops when he hears the clattering of a glass bottle. He turns to a cloth draped opening and pushes the cloth aside. Inside, a little girl sits on the floor staring defiantly up at him.] He took me into his home. [Young Karai practices alongside Shredder.] He allowed me to train alongside him. And thus I learned the art of ninjutsu. I respected him and he trusted me. [An older Karai pulls back an arrow on a bow. She fires several times at him and he bats aside each arrow. [A grown Karai, in full ninja garb, kneels before her master.] To me, he was Oroku Saki. He was more than just my master. [He presents her with a sword.] He became my father.
Back to the present.
Karai It was his destiny to find me. It became my duty to serve him. As it became your fate to slay him. But we are all servants of fate.
Leonardo I’m not so sure. Master Splinter says we are free to decide our own paths. That our lives are dictated by our choices.
Short Aide They are here, Mistress.
Donatello Looks like your plan is working.
Karai So far, but one must always plan for the unexpected.
Leonardo That’s why we’re here.
Karai Yes. Now conceal yourselves and let us see what fate awaits us.
Casey and the turtles run to hide and Karai places Shredder’s helmet back on her head.
Fake Shredder Prepare yourselves.
The Mob Boss enters the dojo with several of his men. He is aiming a rocket launcher at Fake Shredder.
Mob Boss Steady, boys.
Karai, as the fake Shredder, pulls her sword, as do her two aides. She turns to see Hun and the Purple Dragons arriving through another door. Hun has his Lars rocket launcher. Both groups approach each other, with Karai in the middle. Suddenly the glass windows are shattered and Foot ninja arrive on the scene. There is an explosion of smoke, and when it clears, the four Foot Elite stand in front of the ninjas. The turtles and Casey watch from their perch on an overhead rafter.
Michelangelo You know, this plan kind of stinks. What are we supposed to do again?
Donatello Well, if Karai’s plan works, nothing.
Leonardo She’ll get the Foot and Hun to wipe out the mob. And then she’ll get the Foot and the Dragons to stand down. The war will be over.
Michelangelo That sounds good. And if her plan doesn’t work?
Leonardo Then it’s us against all of them.
Michelangelo Like I said, this plan kind of stinks.
Fake Shredder This war is at an end! I have returned to resume control of the city.
Twin-Blade Elite Master Shredder, we thought you were destroyed. [The Elite bow.] We serve you always.
Hun Master, I remain your servant, as will the Purple Dragons.
Fake Shredder Good. I command you to rid me of this pestilence.
Fake Shredder points her sword towards the mob.
Dragon Face Yo! Wait a minute! This ain’t right! We wanna take over Shredder’s turf, not get it back for him.
Hun Traitor! You dare!
Mob Boss Shredder, we have a saying in our family. But you’ll never live to hear it! Fire!
The mob begins shooting.
Hun Purple Dragons, take ‘em out!
Dragon Face Forget Hun! Every man for himself!
Hun and most of the Dragons fire on the mob.
Mob Boss Go, go!
The Foot and the Elite surround the Fake Shredder.
Twin-Blade Elite Foot, protect your master!
Dragon Face fires at the mob, hitting the wall behind a group of them. The wall falls, taking the mob men down. Some of the Dragons are hit and Hun fires his rocket launcher, taking down another group of mobsters. The turtles jump from beam to beam as the wild shooting hits the ceiling.
Hun Yo, Dragon Face, catch!
He turns and fires his rocket launcher directly at Dragon Face, who dives onto the floor. The rocket hits the wall. Dragon Face stands up and fires his own smaller rocket at Hun, who fires again at the same time. The two rockets hit each other and loudly explode. Groaning, most of the fighters lie injured on the floor.
Leonardo Looks like her plan is going to work after all.
Mob Boss Hey, I almost forgot, Shredder. [He takes out a blinking baseball sized explosive device.] Here’s a little present from your old friend, Baxter Stockman! [He throws the explosive.] Sayonara!
The explosion throws Karai to the floor and her helmet pops off. It comes to rest at Hun’s feet and he gasps, setting his rocket launcher down so he can pick up the helmet.
Hun Master? [He looks inside the helmet and then over to where Karai’s aides are helping her stand.] Huh...? Karai.
Twin-Blade Elite To impersonate our master is sacrilege. You dishonor him!
He lifts his weapon menacingly.
Leonardo Looks like it’s time for Plan B.
The turtles and Casey leap down. Donatello performs a split kick which knocks down two of the Elite. Leonardo and Michelangelo take on Foot ninja. Karai’s aides attack the Elite, while Karai battle Foot ninja. Hun fires his rocket at Leonardo, who dodges.
Leonardo Whoa!
The Foot ninja fire blow-gun darts at Casey.
Casey Whoa! [He frantically swings his bat and manages to catch all of them. He checks his body and then sees the darts sticking out of the bat.] Woo-hoo!
A Foot ninja kicks him down. The others continue to fight the Foot. A ninja tosses a net over Casey.
Casey Hey!
He falls, completely ensnared. The turtles back towards Karai and her two aides and find themselves surrounded.
Michelangelo Okay, we’re outnumbered, out-weaponed, and surrounded. What do we do now?
Karai We make peace with our ourselves and prepare our bodies for destruction.
The Foot ninja stand aside to allow the Elite to face Karai.
Michelangelo Funny how you didn’t mention that part of the plan earlier.
Tall Aide Mistress, you must leave immediately.
Karai No. I will stay here and see this through.
Leonardo The Shredder may have raised you, Karai, but you’re nothing like him.
Karai How so?
Leonardo You understand honor.
They smile at each other.
Twin-Blade Elite Hun! Eliminate them all, and we will not forget your help when the Elite controls New York City!
Hun That’s the first thing I’ve heard since this stupid war began that makes sense.
He raises his weapon and takes aim. Before he can pull the trigger, a shuriken flies through the air and hits the rocket launcher. Sparks and smoke shoot out of it and Hun throws it at the feet of some Foot ninja, where it explodes. Smoke fills the room and as the Foot ninja stand up, an invisible force attacks, taking them down again. A half-dozen are battered before Raphael comes strolling through the smoke.
Raphael Hey, guys, miss me?
Leonardo Raph!
Michelangelo All right!
The Elite prepare to attack.
Leonardo I thought you were sitting this one out.
Raphael faces off with the spear wielding Elite.
Raphael Well, I calmed down, thought about it, [He ducks several attempted blows.] and realized I was... [He catches the spear on his sai and knocks the Elite down, taking his weapon from him.] ...being an idiot.
Michelangelo You did that... [He takes down the trident wielding Elite.] all by yourself?
Raphael Well, I kind of had... [He kicks an attacking Foot ninja and socks two others.] a little help.
He lifts his thumb towards some smoke. Suddenly, Master Splinter springs through the smoke, spinning in the air before kicking down two Elites.
Splinter My sons, I was worried we would be too late!
He punches a Foot ninja. The others continue fighting.
Donatello Nah... we had everything under control, kind of.
Karai engages in a fight against the twin-blade Elite.
Karai Turtles, let us finish this!
Shouting, Raphael jumps down in front of  the Elite and he and Donatello bat the Elite aside. Leonardo throws a katana at the Elite, who jumps over it. When he lands, Michelangelo hits him with his nunchaku and Raphael rips the weapon from his hands before kicking him against a support pillar. He slides down. The floor is littered with defeated Foot. One starts to rise, but Karai stomps on him. She approaches the Twin-Blade Elite.
Karai Do you not know this seal?
She presents the medallion bearing the Foot seal. The Elite guard stands.
Twin-Blade Elite Yes. It is the Shredder’s seal. The seal of the Foot.
Karai Then you are honor-bound to obey me for I represent the Shredder!
Twin-Blade Elite We will not!
Karai’s eyes narrow and she lifts her sword. The Elite ducks his head and she slashes down at him. The turtles grimace and close their eyes, and then look.
Turtles Huh?
The Elite’s headgear falls in half and the other Elites gasp. Hun yanks a support post out of the floor and charges at Karai, striking her with it and sending her flying against another support column. Before she can stand, he hits her again.
Hun I will never serve you!
He lifts the post overhead, preparing to strike her again. Two green hands tap his back and he turns to see Leonardo and Raphael. They both punch him and then jump to the side when he tries to hit them with the post. Together they punch and then kick him and he stumbles back towards the broken window.
Hun Ow! [His eyes widen.] Oh, crud.
Shouting, Karai flies at him, her foot outstretched. She kicks him and sends him falling through the window. He shouts all of the way down, landing atop a police car which has just arrived. Other police vehicles pull up to the scene.
Hun Oh!
Karai returns to face the Twin-Blade Elite, her sword pointed at him. The other Elite stand nearby.
Karai Swear fealty to me! Swear it!
Twin-Blade Elite I... I swear, Mistress.
He shouts a command and the other Elite, along with the Foot ninja, kneel and bow.
Casey What’s happening? What did I miss?
Karai walks over to Leonardo.
Karai Thank you. I am in your debt. I shall keep my promise. The vendetta is lifted. The Foot will not take revenge for the slaying of their master.
Leonardo You are honorable, Karai. I know you will keep your word.
Karai You stood with me to the last. All of you have great strength and courage. I hope in the future when our paths cross, we will not be enemies.
Leonardo Only fate can tell.
Karai Regrettably, fate is not the only master we must serve.
She and her two aides bow before leaping through the broken window.
Leonardo Master Splinter, I’m sorry. I just had to do something and--
Splinter It is all right, my son. Sometimes you must follow your heart even if others tell you not to.
Leonardo Thank you, Master.
Cut to a Foot dojo. Karai is seated at a short, wooden table as her two aides approach. They kneel.
Tall Aide All is in readiness, Mistress. We are fully operational.
Karai Excellent. You may leave me now.
They exit and Karai presses a button embedded in the desk. Behind her, one of the wall panels rise. Karai enters a secret room containing medical equipment. At its center is a tall tank filled with liquid. To one side, lying on a couch, is Shredder’s exo-suit, its stomach cavity empty. Karai approaches the tank.
Karai All proceeds as planned, Master.
She kneels. A closeup is shown of the exo-suit and then the tank appears again. Inside, hooked to cables, is the actual body of Ch’rell a.k.a. the Utrom Shredder. Small worm creatures (Biocytes) crawl over its face and body.
Shredder Ah. Good. My body is prepared. And the biocytes have almost finished healing my flesh. Soon I will be myself again. Soon we will destroy the turtles.
As he laughs, Karai looks up with an expression of remorse.

{Roll end credits}

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