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- Ass Pull: Empress form Isis, who pops out of nowhere to defeat Kira. There was no explanation for this whatsoever.
- Fridge Brilliance:
- The reason Konoha isn't as creeped out by the turtles as much as back in New York? Konoha is more used to non-humans!
- Why was Naruto compatible with all of the turtle's weapons? Because he trained with them and has all of their personality traits!
- Hilarious in Hindsight: It makes sense in context that Mikey replaces Naruto as the foolish one.
- Moral Event Horizon:
- Kira's murder on Isis, when the latter was a baby, at that!.
- Neji comes close to crossing this when he tried to kill Hinata at the chunin exams.
- Itachi's massacre of the Uchiha clan. Though it's subverted when he was ordered against his will. His massacre on his own group seems to play it more straight.
- Danzo ordered the Uchiha/Ankoku massacre, sealed Kushina in a root prison for 13 years, and took all of the arms of previous members to attach to his arms.
- Narm: Raph's calling out on Neji sounds more like what the '87 version would say rather than the '03 one.
- Take That, Scrappy!: Sai's absence here was pretty much one for him.
- The Woobie:
- Naruto, Himeko, and Sasuke, all are Last Of Their Own Kind...
- Sakura eventually follows suit, losing her entire family during the Konoha invasion.
- Kushina was one too, being sealed for 13 years.
