The Turtles end up smack dab in the middle of a civil war against the Foot, the Purple Dragons, and the mob as they fight for control of the city. While Leonardo believes they are responsible and must get involved to set things right, Raphael tells him it's none of their business and that they should keep out of it.

''First appearance of Karai''
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!!This episode provides examples of:

* BystanderSyndrome: Raph considers the turf war someone else's problem.
-->'''Raph:''' We shouldn't be here, it's not our fight.\\
''[The Turtles find themselves surrounded by Foot ninjas.]''\\
'''Mikey:''' Looks like it's our fight now.
* ChekhovsSkill: Leonardo is trying to perfect his aim with his katana by hitting the center of various bulls-eyes. Although he repeatedly fails, by the time it comes to using it in battle he hits his target.
* EnemyCivilWar: the Foot Clan, the Purple Dragons and the Mob battle for control of New York following the Shredder's supposed demise.
* EvilLaugh: Stockman over unleashing his new weapon on the Foot. Big Boss finds it rather silly.
* EvilPowerVacuum: With the Shredder gone, 3 factions are fighting for control of the city.
* FamilyFriendlyFirearms: Justified. The Mafia characters are shown wielding such weapons early on, but we later learn that Stockman is providing them with advanced technology to help them go toe to toe with the other two factions.
* HeroicNeutral: Leo and Mikey feel responsible for the gang war and want to help put things right. Splinter and Raph feel it isn't their business and that it's too dangerous to get involved. Donnie is caught in the middle, and while he listens to Mikey's presentation on the issues, never expresses his own opinion on the matter.
* HiddenDepths: Mikey says he understands why Leo thinks this situation is their fault, feeling somewhat responsible himself. He later reveals he's been watching assorted news reports on the subject, which has allowed him to fully work out the current state of the gang war.
* HowTheMightyHaveFallen: The Foot Clan is hit with this hard after the Shredder’s apparent demise. This is symbolized by their new base: a decrepit husk of a building with the only furniture being a couple of mats. Compare this to the Foot’s high-tech skyscraper from the previous season.
--> '''Leo:''' So, this is what happened to the Foot since we got rid of the Shredder? [[LampshadedTrope How the mighty have fallen.]]
* ItsAllMyFault: Leo believes the Turtles, and in particular himself, are responsible for the war in the city.
-->'''Leo:''' I don't get what Master Splinter’s thinking on this one. Do nothing? [[ChronicHeroSyndrome Innocent people are getting hurt]] because of us. [[ItsAllMyFault Because of me]]. I just wish I knew what the shell I was going to do.
* JerkassHasAPoint: The male host of ''Butting Heads'' is very blunt and insulting to his co-host, but he accurately describes the situation as a full-blown gang war between factions vying for total control of the city's criminal underworld.
* KingpinInHisGym: Karai
* LaserGuidedKarma: Three Foot Ninja knock Mikey through a hole in the roof. Raph immediately returns the favor by crashing into them and then uses them to break his own fall.
* LetsYouAndHimFight: The second time Leo and Raph fight against each other.
* MobWar
* MoralMyopia: Leo is so caught up in his perceived moral obligations to the situation that he repeatedly says he can't even ''understand'' why Splinter doesn't want them involved or where he's coming from. Leo himself ''should'' be able to at least see that it's a complex and potentially dangerous situation for them, even if he ultimately decides it's worth the risks, but either doesn't realize or doesn't care about those factors.
* MyGodWhatHaveIDone: Leonardo has this reaction when seeing different news shows covering the gang war, particularly when one reporter says several civilians got injured in the crossfire of one brawl.
* NiceJobBreakingItHero: Leo believes they've caused the war due to taking out the Shredder.
* NoHonorAmongThieves: Leo and Raph stumble onto a transaction, with the Mafia paying the Foot for some goods. It goes south because (much to Weasel's surprise and displeasure) the Foot Elite Ninja opts to count the payment before handing over the goods. Finding only half the agreed upon payment in the briefcase, the Elite orders the mooks to kill the mobsters.
* OOCIsSeriousBusiness: Leonardo ignoring Splinter's orders to just do nothing by walking out of the lair.
-->'''Mikey:''' [[OhCrap Dude!]]
* OutrunTheFireball: When Leo fails to defuse the bomb.
* PlanningWithProps: Acting as MrExposition, Mikey uses a map of the city, and some toys, to determine and demonstrate the EvilPowerVacuum going on in New York City to Donatello.
* SawItInAMovieOnce: Don tries one of his favourite [[Film/TheMatrixReloaded movie]] stunts, only for it to fail miserably in 'real life'.
* ScrewTheRulesImDoingWhatsRight: Leo goes out to help resolve the gang war, even when Master Splinter tells him not to.
* ShoutOut: In the beginning, when Raph and Leo are traversing through the city
-->'''Raph''': Just your [[ComicBook/SpiderMan friendly neighborhood Turtle Man]].\\
'''Leo''': You look more like [[Franchise/{{Tarzan}} Raph-zan, Lord of the Jungle]] to me.
** Don later attempts a stunt straight from ''Film/TheMatrixReloaded''.
* TeethClenchedTeamwork: Big Boss freely admits that he hates Stockman, but he'll gladly follow his battle plan if it means taking down the Foot and the Purple Dragons.
* TimeBomb: Leo fails to defuse one of these in the warehouse and has to OutrunTheFireball.
* TrueCompanions: While the family is divided on whether to get involved at all, the brothers still ultimately go out and support Leo, because they don't want anything happening to him from trying to take it on alone.
* VillainTeamUp: Having no love for the Foot or the Purple Dragons, Stockman has allied with the mobsters.
* WasItReallyWorthIt: When the building is coming down at them at the end, Raph bitterly tells Leo he hopes it was worth it "doing the right thing".
* WhamShot: How Stockman is revealed as the Mafia's tech supplier.
* WideEyedIdealist: The situation hits Leonardo so hard because he genuinely thought things would get better without the Shredder around, only to see innocent people getting hurt during a gang war.
* WrongGenreSavvy: Don tries a move he's seen on TV, only for it to fail miserably in 'real life'.
* YourTelevisionHatesYou: While watching TV, Leo gets constantly reminded of the gang wars that plaguing the city, and how innocent people are getting hurt due to get caught in the middle of the violence.
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