Intro: Raphael voice-over reviewing the preceding two episodes, ending with where we left off last episode – Karai holding a blade at Leo’s throat!
Act 1: Karai orders the TMNT and Casey to drop their weapons so they can talk. Jones, Mike and Don comply, but Raph is very reluctant and Karai reminds them that she will kill Leonardo. Leo tells his brother not to do him any favors and Raph angrily throws his sais, which stick into the ground inches from where Leonardo is pinned. Karai lets Leo stand and explains that she represents the Japanese faction of the Foot Clan. The foreign Foot had intended for the three warring factions (mobsters, Foot and Purple Dragons) to destroy each other, but the fighting was creating too much collateral damage to the City, thus Karai was sent to clean up the mess. She asks the Turtles for their help, saying that the Foot’s vendetta against Leo (for killing the Shredder) will end if the TMNT assist her efforts to restore order.
The guys huddle up, Leonardo suggests that the truce may make reparations for the problem that they created after removing Shredder from power. Raph states that there's no way that he will team-up with the Foot Clan and storms off. As he walks away, Raphael asks Casey to join him, but Jones crosses his arms and says that he's staying - he was taught that when you make a mess, you clean it up. Raph growls "Whatever" and disappears into the dawn.
Karai and her two assistants form a partnership with Leo, Mike, Don and Casey. Karai immediately begins to explain her plan of action to them...
Later that night we see a group of Elite Ninja on a rooftop. Suddenly, the Shredder appears on a building across from theirs!
Act 2: The Elite Guard are shocked to see their master and bow to him. Shredder orders the Foot to follow him.
On the streets below, Baxter Stockman punches his way through the roof of the crashed truck and emerges from the vehicle with the mob's Big Boss. The gangster begins to make plans on how to win the war when Hun and the Purple Dragons show up. Big Boss attempts to sweet talk the gang, but before he gets started, the Shredder arrives on a nearby rooftop. Upon seeing his nemesis, Baxter begins to freak out, fearing that he's going to be slain. However, Shredder merely orders Hun and the Dragons to follow him and they all depart. Stockman begins jumping for joy. Several limousines arrive and Big Boss joins Weasel in the front car - the gangster orders his men to follow the Shredder so they can end this war once and for all. The limos zoom off.
Cut to the Shredder returning to the nearly destroyed Foot HQ. Inside the rooftop dojo, Shredder meets the three Turtles and Casey. We discover that the Shredder is actually Karai in disguise, wearing her master's armor and using a computerized voice synthesizer to imitate his speech. Karai states that the plan worked perfectly and the Foot and Purple Dragons will arrive soon. Leonardo asks how she could ever serve someone as evil and dishonorable as the Shredder, and Karai reveals that Oroku Saki (the Shredder's alter ego) took her in after she was abandoned by her parents. Saki trained Karai in ninjitsu and he became like a father to her - thus she served him without question.
Back to the present… and the showdown. The mobsters arrive first, with guns in hand. In short order the Purple Dragons show up holding their weapons on the gangsters. Following the Dragons, a large contingent of Foot ninjas crash through the thin walls , creating a huge stand-off. The three Turtles and Casey watch the scene from rafters high overhead, waiting to see if they'll be needed. Mikey isn't happy with Karai's plan...
Act 3: The mobsters open fire on Shredder and the Elite. The Dragons open fire on the mobsters. A chaotic fight ensues with all sides taking causalities. The mobsters decide to retreat, but before they leave, Big Boss pulls out a grenade and tosses it at the Shredder. The explosion knocks “his” helmet off and reveals Karai to the Foot and Dragons! The leader of the Elite Guard is outraged that Karai would impersonate their master and vows that they won’t follow her… Hun comes to the same conclusion and they all attack Karai and her aides. Thus “Plan B” is put into effect: the Turtles and Casey leap down from the ceiling shadows and join the fight.
The battle doesn't go well for our heroes as they're so outnumbered. The Turtles, Casey, Karai and her two aides are completely surrounded by the Foot and the Dragons. Casey is ensnared by a net and falls to the floor. Mikey wonders what they should do, and Karai tells him to make peace with himself and prepare to die - Mikey groans that she didn't tell him that was part of her plan when this all began...
Act 4: The Elite Guard tells Hun that if he finishes off the TMNT, the Foot will reward the Purple Dragons once they regain control of the city. Hun states that this is the best thing that he's heard all day and takes aim at the Green Team. This angers Dragon Face, who bellows that the city was supposed to go to the Dragons, not the Foot. Dragon Face tells the gang members to forget Hun and it's every man for himself. Hun lifts his gun, but before the hulking hood can fire, a shuriken arcs through the air and smashes into the weapon, causing it to short circuit. Hun tosses his gun aside and it explodes, creating a cloud of smoke. Several Foot ninjas are attacked and defeated before the smoke clears, and a shadowy figure emerges from the haze - it's Raphael! Leo and the others are shocked and overjoyed to see their brother! Raph explains that he did some thinking and came to the conclusion that he was being an idiot. Mikey asks if he arrived at that conclusion on his own, and Raph reveals that he had some help. Cue Master Splinter, who leaps into the room and begins taking down Foot ninjas.
The tide of battle turns with the arrival of Raph and Splinter. Karai gets the drop on the leader of the Elite Guard and holds her blade at his neck, forcing him to swear fealty to her. Hun is still active and he grabs a girder and smashes the female ninja with it. The Turtles attack and their blows cause Hun to stumble backwards towards an opening in the wall - as he struggles to regain balance, Hun sees Karai leaping towards him. The Foot leader kicks Hun out of the opening and he falls to the ground below. Fortunately for the massive Purple Dragon, the police begin to arrive and one of their squad cars breaks his fall.
Karai thanks the Turtles for their help and states that the Foot will bother them no more. Leonardo compliments her and states that while she worked for Shredder, she is nothing like him: she knows the meaning of honor. Karai bows and leaves with her assistants.
Leonardo apologizes to Master Splinter for disobeying him, but the Sensei pats his son on the shoulder and tells him that it's okay, sometimes we must follow our hearts, even if others tell us not to.
Later, Karai is seated at a large wooden desk in a dojo. One of her aides reports that everything is now in order. The woman excuses her assistant and then heads into a secret room, a Foot medical unit. Inside we see the exo-suit body of Oroku Saki laid out on a couch, its stomach cavity empty. Karai bows in front of a nearby tank containing a strange crimson fluid and the body of the Utrom Shredder! Small worm creatures (Biocytes) crawl over its face and body and it announces that it will soon be healed. Once fully recovered, the Shredder swears vengeance on the Turtles! Karai raises an eyebrow at this announcement as her mentor laughs maniacally.