The Turtles have been struggling with the concept that they may need to kill Shredder in order to prevent many more deaths. This ideological conflict has now bled into their current battle. Shredder is a calculating man bent on domination, whereas Slash is a beast who is a victim of his own circumstances. The boys are split between how to deal with their new adversary; is killing him justified or is simply stopping him enough?
This internal schism in the group is taking the Turtles in a more mature direction than most previous iterations. Surprisingly enough for such an action-oriented franchise, killing has been avoided most of the time. Many times the violence would be against robots or their weapons would be used defensively.
It is refreshing to see these characters struggle with issues larger than what toppings to get on pizza. The fallout of this battle leaves things unresolved as the brothers appear to be drifting apart.