The episode starts with some Kraangdroids patrolling the street, while Ivan Steranko watches from a corner. Then Ivan heads into their hideout where Anton Zeck is also hiding. Zeck complains that they need to leave the city and that their food supplies are very low. Steranko agrees, but escaping is nearly impossible since the city is heavily guarded by Kraangdroids. Zeck fears that if they get captured, they may get mutated. But Steranko refuses to get mutated and has a plan to get out of New York: They will find and capture Karai so that they can make a deal with the Shredder: They will trade her for safe passage out of the city.
Over at Antonio’s Pizza-Rama, Michelangelo, April and Splinter clean and tidy up their new temporary home. Mikey then notices that Splinter is obviously preoccupied, though he simply says that his thoughts are elsewhere. While at the back of the building, Donnie is busy working on a retro-mutagen to transform April’s dad, Karai, and other affected people back into humans, but it’s not ready yet. Just then, Leo, Raph and Casey return from a stealth mission from the old lair. They got some chemicals for Donnie’s experiments, a TV for Mikey and Splinter’s family picture. As he looks at it, the Turtles’ sensei remarks that his family can’t be complete without his daughter with him. Everyone resolves to find her, and when Raph mentions that she might have been captured by the Foot or the Kraang, Splinter says he saw her on the streets recently, but he was not in his right mind at the time and couldn't help her. The Turtles are ready to start the search now, though Leo tells April and Casey they need to stay behind.
Meanwhile over at his lair, Shredder is also looking for Karai, and he’s not happy that Fishface and Rahzar have been unable to bring Karai in. He threatens to turn them over to Tiger Claw if they can’t get the job done.
Aided by a DNA tracker that Donnie has whipped up, the Turtles are able to find some snake scales (which Mikey unfortunately mistakes for potato chips). Zeck and Steranko find Karai first, but the Turtles show up in the nick of time, and fight. During the battle, Steranko lines up a shot at Karai with a tranquilizer gun, but Raph knocks him off-balance and he misses. The shot spooks Karai enough to make her flee the scene, and the Turtles have to sneak past a host of Kraang forces before they track her to a warehouse.
Kraang droids make it inside the building, too, but Karai makes short work of them. The boys try talking to Karai, and when she sees Leo, she’s able to focus long enough to transform back from snake creature to something close to human. Leo asks her to return with them, but she says it’s too dangerous. Just then, Fishface and Rahzar arrive, stunning Karai with a taser and keeping the Turtles at bay with a poisonous smoke bomb. The mutants get Karai out to a motorcycle outside the warehouse, but while they bicker over who should get to turn her over to Shredder, Zeck sneaks up and steals the bike with Karai still on it. Zeck brought Karai to Steranko. He then calls Shredder to arrange a meeting at the docks. Unknown to them, one of Donnie’s cyborg roaches is on his shoulder, allowing the Turtles to eavesdrop and hear the plan.
Down at the docks, the meeting goes down as scheduled, Zeck and Steranko proposing that the Shredder provide them with a safe passage out of the city in exchange for Karai's well-being. The Shredder, after arriving with Fishface and Rahzar as backup, remarks that he doesn’t make deals, but will make an exception in this case. His proposal of allowing Zeck and Steranko to leave this encounter alive if they give him Karai is interrupted when Leo shouts out, making the predominant offer: If they free Karai, he'll let all of them walk away with their lives. Both Leo and his brothers leap down to battle the Shredder while Fishface and Zeck face off and Rahzar and Steranko face off, Karai caught in the middle of their confrontation. The Turtles manage to put up a good fight against the Shredder as they score some hits on him, Mikey, Raph, and Leo managing the majority of them. After being knocked into a cargo container, Leo manages to kick both Rahzar and Steranko away from Karai and manages to free her from her restraints with a Katana. He then encourages her to flee while she has the opportunity, whereupon Karai motions to the east toward the city and utters the word “comet” before heeding Leo and escaping into the ocean. Leo begins to puzzle over what she could've meant by that word, while the Shredder rants about the departure of his surrogate daughter. Leo quickly throws smoke bombs in his face, allowing himself and his brothers to escape, leaving the Shredder thoroughly upset. Turning to see that Fishface and Rahzar have captured Zeck and Steranko, the Shredder has his two lackeys take them to Stockman's lab, insisting that someone must pay for the events that have unfolded today.
The Turtles emerges from the docks. Raph complains that they almost had Karai, but Donnie explains that it was too dangerous. Leo tells them that Karai gave him a clue on where she is hiding, as they look towards the east of the city, wondering what she means by "comet."
Meanwhile at Shredder's Lair, Zeck and Steranko were brought to Stockman's lab, where it is revealed that Stockman has prepared warthog and rhinoceros DNA for use in mutating both Zeck and Steranko. Rahzar and Fishface poke fun at the unfortunate duo over their "choices" of mutation, with Fishface sarcastically commenting about the "excellent" DNA that has been selected for them and Rahzar laughing hysterically that Zeck will be turned into a warthog. Zeck yells in fear that he's too handsome to be a mutant. Shredder enters stating that their fates has been sealed. He mutates Zeck first, because he stole the Kuro Kabuto. Steranko watches in horror as Zeck is mutated into a warthog. When it is Steranko's turn to be mutated, he references Shredder about their "friendship" and claiming he'd be more useful as a human than a mutant. But his pleas are not heeded, and he was mutated shortly into a rhinoceros. In the end, both Zeck and Steranko bellowing into the sky in pain, confusion, and anger at being turned into "freaks".
"Anton Zeck - I'm starving, all our food is gone and we're down to moldy ketchup and dead cockroaches!
Ivan Steranko - Secret headquarters, mine. Moldy ketchup cockroaches, mine!"
"Fishface - Eh, Master Shredder, Karai is just to scaly... I-I mean, stealthy. And the city is so big.
Rahzar - She's as slippery as a serpent... Hm, I mean... we looked everywhere, master."
"Steranko - This is funky fresh. Snake skin, recently shed, I'm better hunter than my brother Boltak.
Anton Zeck - Stop messing with that butt-nasty skin, put you eyes right down there, son. The beast is hiding.
Ivan Steranko - Da, now I go make her sleepy nap time. Steady... Steady... Turtle face? Mother Russia!"