The episode starts inside a dungeon where Karai continues scraping a coin against a cell bar. Suddenly, Fishface enters and delivers a bowl of food to Karai, who sarcastically mocks him of the food she's been given because he's not in charge and follows Tiger Claw's orders, much to Fishface's ire whilst the teen girl smirks. After Fishface storms out, Karai finally breaks a cell bar and tries to escape. After busting open her cell door, Karai makes a dash to the Dungeon's exit and slices the lock in half with the cell bar, only to be grabbed on the head by Tiger Claw when she thinks she's reached freedom. Karai makes good use of the bar as she attacks Tiger Claw with it, but she is disarmed and a powerful blow from Tiger Claw knocks her unconscious. As Tiger Claw is about to end her life, the Shredder intervenes and orders Tiger Claw not to. Karai wakes up a short while later, only to find her wrists chained with shackles. Shredder approaches her, much to her ire, and, removing the lower part of his mask, calmly tries to explain to her that whatever he did was for the best, before asking why she is so belligerent against him. After Karai quietly fumes, Shredder curiously asks if she has anything to say, and calls her 'daughter'. Furious upon hearing this, Karai harshly berates him, angrily screaming that she is NOT his daughter.
Meanwhile, in the Sewer Lair, the Turtles are trying to plan the best possible way to rescue Karai successfully. Raph says that he is on board for saving her, but also wants to take down the Shredder and his forces once and for all to make their attack on the Shredder's lair tenable. Leo comments that it would be too risky to confront the Shredder in the way that they did last time. He then advises that each brother take on a specific position to ensure that their mission is successful. Mikey disagrees with this and Master Splinter, intruding on the discussion, proclaims that disagreement should never precede a mission. He then asks Leo if he can talk to him. He tells his son that it would be difficult - if not impossible - to avoid putting his and his brothers' lives at risk if they try to save his daughter. Leo wants to believe that the mission has purpose if Splinter ends up reunited. Splinter replies that he's not willing to risk the Turtles' lives for his daughter's. Leonardo (conflicted) agrees before walking back to his brothers and telling them that Splinter isn't right. With this, the brothers decide to depart to the Foot HQ, with all of them playing an important role in the rescue operation. Mikey is to distract the Shredder's henchmen (Fishface and Rahzar) with his shadow puppetry skills and Leo and Raph are to infiltrate the Dungeon through the sewer system, all while Donnie disables the power to the building by cutting down a couple of power lines. Raph and Leo quickly locate the Dungeon and, after ambushing two Robot Foot Soldiers, they reach Karai's cell. Karai tells Leo that it took him long enough' and Leo replies that they got a little tired of waiting for Karai to escape on her own time. Receiving demands from Raph to hurry up, Leo breaks the lock with a pair of small metal weapons before freeing Karai. Karai grabs a Katana from a fallen Foot-Bot, but Leo, Raph, and Karai run into trouble; Tiger Claw. The Turtles and Karai charge at him, but they are outmatched, as Tiger Claw's skills are still sharp. Meanwhile, Mikey leads Rahzar and Fishface to the top of the building where he actually manages to beat them in battle. However, to Mikey's victory comes the expense of an injury to his arm. Meanwhile, Leo calls Donnie on his T-Phone and orders him to activate a dog whistle, hoping that Tiger Claw will hear this and be defeated. Tiger Claw is caught off guard by the sound, allowing Raph to knock him down. Karai steps over him, warning him that none of this is over.
The team members regroup on the surface and are met by Mikey, who they comfort because of his arm wound. However, this proves to be the least of their worries, as numerous Foot-Bots leap down from the top of the building and surround our heroes in the street. Tiger Claw soon reappears and tells the Turtles to surrender, as they don't pose a chance and will be outmatched. However, Donnie then rams the Shell-Raiser right into the squadron of ninjas and has both his brothers and Karai board the vehicle. As Karai boards, however, she notices that the Shredder is staring down at her from the top of the building with a cunning expression on his face. Nevertheless, the team starts to drive away, but the Foot-Bots reassemble and begin to use their weapons to drill into the Shell-Raiser with the intention of retrieving Karai. The Turtles quickly outsmart the robots, only to realize that Tiger Claw and a large army of Foot Soldiers are pursuing them on Dragon choppers. Raph prepares to thwart off their pursuers with their supply of manhole covers but realizes that they have used them all up and asks who forgot to refill them...to no avail. As the team resorts to the garbage cannon for defense, Karai asks Donnie if there is anything better that they could use, to which Donnie responds by revealing a plethora of the Shell-Raiser's weapons, a few of which he uses against the pursuing Foot Soldiers. Discombobulated from a blast of smoke from the Shell-Raiser, the majority of the Foot Soldiers give up the chase, but Tiger Claw continues and uses his jetpack to land on the Shell-Raiser, which he stabs his sword through and nearly hits Karai. Karai faces off with Tiger Claw on the top of the vehicle, putting up a good fight, but eventually getting bested by him. However, the Shell-Raiser then drives below the roof of a building and Tiger Claw cannot avoid colliding with it, resulting in him falling down in defeat. This allows time for the Turtles to hide their vehicle and then proceed to the Lair. during this time, Karai becomes filled with great remorse and tries to apologize to the Turtles (especially Leonardo) for her previous nasty mistreatment, treachery, and cruelty towards them as well as thank them for rescuing her. However, Leo generously forgives her, knowing that she isn't good at saying this. She reciprocates Leo's affection with a warm smile.
Once they have reached their home, Raph mends Mikey's wound as Donnie chugs a milk carton while Leo asks Karai if she is willing to stay with them for a while. With the Shredder going after them all, Karai says that it is her only choice and admits that their lair is ''not so bad''. Mikey proposes having a 'family' hug, only to decline because of his arm. Splinter then enters the room and, after hearing about the incident that Mikey had, begins to scold the Turtles for not following his orders, but he then notices Karai, much to his gratification. Without a moment of hesitation, Karai walks over to Splinter and hugs him, causing Splinter to believe that some things may very well be worth a risk.
Later, Tiger Claw reports back to the Shredder, stating that he has scoured the city in search of Karai and has ordered some Foot-Bots to keep up the search and return to him with every detail. After Tiger Claw reveals that, so far, he has turned up empty-handed, the Shredder tells his minion that his efforts are pointless and that he was always counting on Karai's escape. He then goes on to state that Karai will probably arrive with Splinter and his pupils to finish what they have started, which would allow the Shredder to have his vengeance. The Shredder then demands Tiger Claw to tell Stockman-Fly of the situation.
In the Lair, Karai begins readjusting to her new lifestyle with her biological father Splinter, as she watches the Turtles (who are now her adoptive brothers) undergo some casual sparring while she takes time to observe. Donnie and Raph square off while Leo and Mikey face-off, with Mikey goofing around such as tucking his limbs into his shell and rolling on the ground, catching Leo off-guard. Leo tells Mikey to concentrate, swinging his sword while Mikey effortlessly dodges all of this and smacks Leo on the face before getting kicked to the ground by Leo with a roundhouse kick. Mikey complains about his poor arm. Leo immediately apologizes. With his brother thrown off guard, Mikey, using his dominant uninjured arm, quickly flings a large water balloon that hits Leo right in the face. Additionally, Mikey embarrasses Leo in front of Karai, who snickers in amusement while Splinter face-palms in dismay, all of this to Leo's chagrin. Leo blushes in embarrassment because he still has feelings for her, even after he insisted he disliked her in "The Alien Agenda".
Leo angrily charges at Mikey and tackles him to the ground. As the duo tussle, Donnie accidentally gets swept up in the brawl. Raph watches the horseplay for a few seconds as the three brothers tumble across the dojo with a confused look on his face, only to shrug (as if to say 'Eh, why not'), drop his sais and charges at them to form a doggy pile on the floor. Amused by this more than ever, Karai curiously, yet amusingly asks Splinter if this happens on a daily basis, at which point Splinter has seen and heard enough, telling every one that the training is finished for the day. The Turtles then head into the living room to relax , while Karai stays with Splinter for several minutes. She glances at the picture of herself (as an infant) in Tang Shen's arms and then asks Splinter what really happened between him and the Shredder, as she was never told.
Splinter explains that their rivalry wasn't only sparked by their simultaneous love of her mother, but something deeper. He tells her that there were battles between the Hamato Clan and the Foot Clan that lasted for centuries. One day, after the Foot Clan was defeated, Splinter's father found Oroku Saki (the Shredder) as an infant that had been abandoned. Splinter's father decided that he should give Saki shelter and Oroku soon met Hamato Yoshi (Splinter). After this occurrence, the two children grew up alongside each other, behaving like best friends but also engaged in sibling ribaldry as brothers are. However, that minor rivalry began to grow when the two of them learned of their mutual love of Tang Shen. Not long after this, however, Saki learned about the clan that he originated from (the Foot Clan) and was shocked when he figured out that Splinter had kept it secret. This, plus the fact that Shen had sided with Yoshi, caused Saki to initiate a fight with Yoshi, tearing through the dojo that they trained in, ending with the loss of Shen, who took a fatal blow meant for Splinter. With the dojo ablaze after candles were struck down, Saki found Karai unattended outside, taking her away and rebuilding the Foot Clan in his quest for power. Reverting back to the present, Karai becomes angered upon hearing all of this and asks her father about revenge and why he doesn't seek it, even adding that Splinter could take out the Shredder. Splinter explains that revenge is something that can always lead to more pain - something that the Shredder doesn't realize. He then says that being reunited with Karai is far better than anything else. Each of them then enjoy a cup of tea, though Karai sips her bowl reluctantly.
Soon, the four turtles prepare to go to bed, while Karai already appears to be asleep. Just to make sure of this, Leo asks if she is awake, but he does not receive a reply. Thus, he exits the room that she's lying down in. However, Karai then opens one of her eyes, revealing that she was simply pretending to sleep. Cut to a scene of her about to leave the lair via the abandoned subway tracks when Leo approaches her and informs her that going after her true enemies alone is like a death sentence. Karai warns Leo not to stop her, but Leo replies that he only wants to help. Karai tells him that her whole life has been about revenge and having Leo assist her in it wouldn't be right. Leo once again tells Karai to let him help. In response to this, Karai seductively approaches Leonardo, puts her palm on his shoulder, leans in close to his face (as if they were going to kiss) and smiles. (Leo looks shocked) but instead she flatly rebuffs his offer and tosses a ball of blinding powder in his face after apologizing. After Leo tumbles over, Karai departs down the subway tunnel, claiming that 'this will end tonight'.
Sneaking back into the Shredder's headquarters, Karai notices that her former 'father' seems to be sitting in his throne, but after coming closer, she realizes that the Shredder has put Chrome Dome there instead. The Shredder then appears from out of the shadows and says that she's returned sooner than he expected. Chrome Dome then grabs Karai from behind, but she manages to impale it with her blade. She then confronts the Shredder in combat, vowing to destroy him for what he's done to her father. Vaulting at the Shredder, Karai attacks, but the Shredder tells her that she's made a bad mistake and that she holds no surprises for him, since he taught her everything she knows. Karai attacks the Shredder from every angle, but her rage leaves her vulnerable to one of Shredder's attacks and she is easily defeated by the person that taught her Ninjutsu. The Shredder hands Karai over to Tiger Claw, who reveals that the Turtles haven't been spotted yet. Commenting that they can't be far behind, the Shredder delegates a large horde of his henchmen to take Karai to a place where a mysterious experiment will happen. Meanwhile, Leo awakens near the entrance of the Sewer Lair and his brothers and sensei walk up to him, whereby he tells them about Karai's decision to take revenge. Splinter then calls himself a fool and fears that he told her too much too quickly. While in the Shell-Raiser, near the Foot HQ, they manage to see Karai being transported somewhere by the Foot. Leo quickly tells Raph to fire all of their weapons at once. Knowing that this could harm his daughter, Splinter tells him not to and says to move the Shell-Raiser in closer, but not to the point where the villains can spot them.
Inside Stockman-Fly's lab, the Shredder walks in and it is soon revealed that Stockman-Fly was told to extract a large portion of DNA from a serpent and place it inside of his vat filled with Mutagen. The Shredder then orders his men to have a gagged Karai bound to a table inside of a cage hanging over the vat. Tiger Claw comments that the Shredder is pretty ruthless if he wants to have his own 'cub' get mutated, but the Shredder replies that he has no intention of mutating Karai. His plan is that, when one or two of the Turtles attempt to save Karai, he will rapidly kick them into the Mutagen, which would make them become brainless serpents that would immediately start to target Splinter. Therefore, the latter would be left completely mortified and the Shredder would get the chance to 'shatter' his body. However, what Stockman-Fly did not reveal is that, when the Shredder entered, he accidentally spilled a mysterious chemical into the jar that contains the modified Mutagen after having been startled his master's voice. Regardless, he states that everything has been perfectly prepared. The following moment, Splinter and the Turtles all jump down from the ceiling. It is not long before Donnie, Mikey, and Raph all become trapped inside of spring-loaded cages that were set on the floor, while Master Splinter is restrained by ropes that the Foot-Bots wrap him up with. Leo is also tossed into a cage by a Foot-Bot, but, luckily, just as the cage retracts on top of him, his katana gets caught in it and he pries his way out. He climbs up the chain that Karai's cage is attached to and is able to reach her. He removes the duct tape from her mouth and she thanks him for this. However, the Shredder then tries to stab Leo from behind, but Leo's duck results in the Shredder's gauntlets accidentally cutting through the chain stabilizing Karai's cage. Leo and the Shredder both jump clear of the vat, but Karai obviously can't, and her cage sinks deep into the Mutagen, Master Splinter observing in fear. The cage comes flying out of the vat and Karai emerges shortly thereafter. When the Shredder sees this, he is filled with quite a lot of remorse.
Karai drops from the very edge of the tank, and Splinter frees himself so that he can catch her in his two arms. She is now a swift viper-like creature with hands that resemble miniature versions of her reptilian head. During the following chaos, some oil is leaked all over the ground and it comes into contact with electricity from a destroyed Foot-Bot, causing a large fire to ignite. The Shredder immediately tries to pin the blame on Splinter for Karai's mutation, and Splinter bears a furious expression on his face as the Shredder charges at him. However, the Shredder is halted when a large piece of the ceiling caves in, separating him from his enemy. Tiger Claw walks up to the Shredder, telling him that they have won this fight and should retreat proudly. He then questions Tiger Claw's statement, as, for the first time in years, he feels like he really has been defeated. Karai, one of the few people he's ever grown fond of, is now mutated, and he refuses to take responsibility for his own act. Once again, he creates a new vow of vengeance, before finding a gap in the debris and disappearing into it. Meanwhile, Karai 'awakens' after her transformation, continuing to unleash her rage on everyone around her. She wraps her tail around Splinter's body, thinking him to be food, but Splinter decides to quickly remind her that he is her father and this instantly causes her to release him from her grasp, before spitting venom right between Raph's eyes and then slithering out of a nearby window in guilt. All of them are then forced to escape before Baxter's laboratory goes up in flames.
Failure hits each and every one of the Turtles hard, especially Leo, who says that he should've stopped the Shredder when he had the chance. Then, they follow their silent sensei all the way back to their lair. Mikey asks Donnie if, someday, he will be able to develop another Retro-Mutagen to turn Karai back. Donnie hopes that he will be able to. On a rooftop in the city, Serpent Karai climbs over a billboard and falls, before shapeshifting back into her human form. After this happens, she smirks and then hisses at the screen, ending the episode. Only her serpent eyes and fangs give clues to the fact that she is still a mutant...
"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) Karai - HISSS!!"
Donnie gets trapped in a cage, but he is shown helping Leo free Raph and Mikey after Karai mutated and neither Leo nor Splinter had freed him. It is possible he took a page from Leo's book, grabbed his bo staff, and used the blade to free himself.
Donnie slices a Footbot in half, but he somehow did so without using his blade.