The Turtles ended up struggling against the Foot, the Purple Dragons, and the mob as they continue to fight each other for control of the city. Even bigger troubles come up when the Shredder's successor, Karai, clashes with the Turtles.
This episode provides examples of:
- Bus Full of Innocents: Who inevitably get caught in the crossfire...
- Enemy Civil War: the Foot Clan, the Purple Dragons and the Mob battle for control of New York following the Shredder's supposed demise.
- No Good Deed Goes Unpunished: Mikey's opening narration in eliminating the Shredder.
- Mob War
- The Starscream: Dragon Face tries to rebel against Hun, but fails.
- Jerkass Has a Point / What the Hell, Hero?: Raph's attitude during the City at War trilogy. What the Hell, Hero? stems from the fact that he refuses to believe that the turtles were responsible for New York's gang war between the Foot Clan, Purple Dragons, and the Mob and he sounds like he doesn't care about the innocent people who have been caught in the crossfire. This stems from his statement that the turtles' involvement would only "add fuel to the fire", in other words, make the situation worse and to be honest, Raph wasn't wrong, apart from Leo saving a gang of mobsters from an exploding warehouse and evacuating a man trapped in a bus, the turtles weren't making much progress to ending the war until Karai showed up.
- Shout-Out: Mikey makes one to Captain America when he throws a garbage can lid at some foes
- Vapor Trail: A rare example of the heroes getting caught in one, when Stockman's robot ignites the fuel trail leading to the bus Leo and Raph are trapped in.
- Would Hit a Girl: The Turtles have no problem fighting Karai.