The episode starts with Fishface bringing some food to Karai. She makes fun of him because he's not in charge and follows Tiger Claw's orders. When he leaves, Karai finally breaks a prison bar and tries to escape. However, Tiger Claw grabs her and they fight. Karai gets knocked out and when Tiger Claw is about to slay her, Shredder enters and orders him to stop. Karai wakes up chained and Shredder tells her that everything he has done was for the clan's honor and calls her daughter. Karai yells that she's not his daughter.
In the lair, the guys try to figure out a plan for saving Karai. However, they don't all agree. Splinter tells Leo that a plan that leads to confrontation with the Shredder is doomed to failure. Leo says that it is worth it to save Karai. Donnie is left in the Shellraiser to monitor the situation and turns of the power for Shredder's tower. Mikey distracts Rahzar and Fishface with his shadow skills and Leo and Raph sneak in from the sewers and free Karai. Tiger Claw appears and he attacks them. While Mikey knocks out Fishface and Rahzar who scratches his arm, Donnie uses a dog whistle to drive Tiger Claw crazy. Leo, Raph and Karai escape and find Mikey. Then, tons of Foot-Bots appear along with Tiger Claw. Donnie uses the dog whistle to distract Tiger Claw and drives over a few Bots and they escape after a chase.
The Turtles and Karai return to the lair and Raph wraps up Mikey's arm. Splinter asks what happened, only to see his daughter again. She hugs him and Leo says that his plan worked. Tiger Claw returns to Shredder and tells him a few Foot-Bots are still searching for them. Shredder says that he counted on Karai's escape and tells Tiger Claw to bring him Baxter Stockman. In the lair, the Turtles are training as Splinter and Karai observe. Mikey easily avoids all of Leo's attacks and throws a water balloon at his face. To impress Karai, he jumps at Mikey and they roll over Donnie and Raph joins them. The Turtles leave and Karai asks Splinter what happened with him, Shredder and her mother.
Splinter tells Karai of the history between both the Hamato and the Foot and that once Oroku Saki discovered his true origins with the Foot, and discovered that Hamato Yoshi and Tang Shen were together, he sought to revive his true clan and kill Hamato Yoshi, killing Tang Shen by accident and then blaming his rival, burning the house to the ground while taking his only daughter with him.
Angered, Karai suggests that they take the fight to the Shredder but Splinter merely states that being reunited is enough for him. That night, Leo catches Karai trying to sneak out to go after the Shredder by herself and says he wants to go with her. Karai knocks Leo out and continues on her own. When Leo wakes up, he tells everyone what happened and Splinter blames himself for telling her too much too soon.
Karai attempts to murder Shredder in his throne room only to discover Chrome Dome waiting instead. Shredder admits that Karai returned sooner than he expected and shortly defeats her in battle before ordering Tiger Claw to bring her to Stockman's lab, the Turtles and Splinter, quietly following behind them.
Stockman finishes mixing some DNA when the Shredder arrives with the foot and Karai, explaining that she would be used as bait in order to capture the Turtles and mutate them into mindless snakes to use against Splinter, breaking his spirit and then his body. Baxter doesn't let Shredder know that he accidentally spilled in an extra chemical during the creation of the mutagen, and states that everything is ready. Splinter and the Turtles arrive and begin battle. Mikey, Raph and Donnie quickly get trapped in spring loaded cages, while Leo uses his sword to break free of his. Leo manages to reach Karai, only for Shredder to swipe at him, missing him and cutting the chain, watching helplessly as Karai falls into the mutagen, transforming her into a mindless mutant snake and unleashes her rage on all around her. Shredder blames Splinter for what happens but gets blocked off by debris as the building catches on fire. Tiger Claw assures him that they will get revenge and the Foot escape.
Karai wraps around the traumatized Splinter intent on killing him but then she stops, calling him father before leaving. Splinter and the Turtles escape the building and watch it burn before Splinter tells them it's time to return home. Elsewhere, Karai changes back into human form with green eyes and fangs, then turns toward the screen and hisses.
"Karai - I am not your... daughter!"
"Michelangelo - You are looking good, Rahzar! You lost some weight? (Rahzar charges as he scratches Mikey's left arm in slow motion) TO... KKA...!"
"Michelangelo - It's just a scratch Sensei, you should see the other guy."
"Splinter - What have you boys done?! I though I told you...! (he sees Karai) Miwa. (Karai hugs him)
Karai - Father. (Splinter hugs her)
Leonardo - You see, Sensei? I told you my plan would work.
Splinter - Perhaps some things are worth the risk."
"Leonardo - Going after Shredder alone is a bad idea.
Karai - Don't try to stop me, Leo.
Leonardo - I want to go with you.
Karai - What?
Leonardo - You're right. Shredder will never stop hunting us. The only way for us to be safe is to take him down.
Karai - So much of my life has been about revenge. I can't ask you to risk your life, too.
Leonardo - Let me help. (Karai approaches as she leans on him as if she's going to kiss him! Leo looks shocked as he looks around for a while)
Karai - Sorry, Leo. (she punches him, then knocks him out with some blinding powder. Leo coughs as his eyes remain open as he falls. Karai quickly heads to the surface) This ends tonight!"
"Shredder - Karai...
Karai - Shredder... (Chrome Dome quickly grabs her)
Shredder - You have returned sooner than I've expected. (Karai stabs Chrome Dome, destroying it)
Karai - The time has come for me to say goodbye, Shredder."
"Stockman-Fly - Whatever you require, I can create it. More mutagen, a few chemicals, and some...
Shredder - Stockman!
Stockman-Fly - AH!! (his reaction accidentally makes an orange chemical fall in his serpent DNA serum) Oops! Um... that should be okay. Master Shredder.
Shredder - Is the mutagen ready?
Stockman-Fly - Prepared to your specifications. (he flies to the mutagen tank as he pours the serum in) The serpent DNA is ready.
Karai - No! You wouldn't! (Tiger Claw gags her with tape)
Shredder - Make sure she is secure.
(Foot-bot hangs Kari in a cage over the mutagen tank)
Tiger Claw - You are more ruthless than I thought, mutating your own cub.
Shredder - I have no intention of mutating her, she is bait, when the turtles attempt to rescue her I will drop them into the Mutagen. This will mutate them into mindless serpents. (the snake wakes up to see the rat Shredder as thrown in) I want Splinter to witness his pupils become one of the rat’s deadliest predators, then when his spirit is broken I will shatter his body. (the snake strikes the rat with its fangs before eating it)"
"Leonardo - Hang on, Karai! (he gets to the top of Karai in the cage. He removes the tape off her mouth)
Karai - Thanks. (Leo smiles as Shredder suddenly appears)
Splinter - Leonardo! (Leo ducks in time to avoid Shredder swiping him. However, Shredder cuts the chain as he and Leo fall of the edge with Karai falling in the mutagen)
Karai - AAAHH!!
Splinter - MIWA!!!
Shredder - KARAI, NOOO!!! (Leo and Donnie watch in horror. The empty cage is thrown out of the mutagen with a mutated Karai swimming in the ooze before emerging) Karai... (Serpent Karai comes out as she begins to fall. Splinter frees himself as he kills the Foot-bots. He catches his mutated daughter)
Splinter (in sadness and horror) - Miwa... my child... (the mutated Karai wakes up as she attacks Splinter, then she destroys some Foot-bots. Leo and Donnie fight off the Foot as they free Raph and Mikey. However, one of the destroyed robots ignites some oil due to the sparks coming from it, setting the lab on fire)
Stockman-Fly - No! My lab! (Shredder pushes him away)
Shredder - YOU, HAMATO YOSHI, YOU DID THIS!! (Splinter glares at him as Shredder tries to attack, but is blocked) NO!!"
"Tiger Claw - Master Shredder we must go!.
Shredder - Leave me!
Tiger Claw - Splinter will suffer for what has happen today. You have won!
Shredder - Won!? (Looks at Karai in her mutated form)
Shredder - (takes off mask) I shall avenge you, my daughter!
"Donatello - We've got to get out of here!
Leonardo - Not without Karai!
Splinter - Karai, you must listen to me! We must go! (Serpent Karai sees him as she wraps him around in her coils) Daughter... please...
Serpent Karai - Father...? (Splinter makes a slight smile as his daughter releases him. Karai then spits corrosive venom right in Raph's eyes)
Raphael - AAAAHHH!! (Karai slithers way with Leo chasing her)
Leonardo - Wait! (outside, the Turtles and Splinter have escaped. Leo is full of sadness with Karai as a mutant. Donnie is seen with a gourd full of water as he tries to help Raph see again from the blinding venom)
Donatello - Easy, Raph. (he pours some water in his eyes)
Raphael - Enough! I can see fine now! (Leo approaches his broken hearted sensei)
Leonardo - This is all my fault. I should have stopped when I had the chance. I'm sorry, Sensei. (Splinter doesn't answer) Sensei?
Splinter - (broken hearted) We should go home, my sons."
"Michelangelo - You can make a retro-mutagen for Karai, right?
Donatello- I don't know, Mikey. I hope so... (everyone leaves, but Leo stays for a while with sadness. Elsewhere, Serpent Karai is seen changing back into her human form with her eyes still remaining as a serpent's. She then reveals her forked tongue and fangs)