Renoir returning to Raphael's lair and asking to be taken back as his student, kneeling down to him... and then Raphael kneels down as well and responds with "Welcome back, my student". Made this troper smile.
Leonardo's friendship with the ninja Sadao. Flashbacks show how rocky (to say the least) their first encounters were. To see how far they have progressed since then, to the point they are implied to often work side-by-side now, is a ray of hope in an otherwise very dark story.
Fan-Preferred Couple: Shadow and Renoir are this to the semi-canon Renoir/Davianna. Shadow and Renoir argue like a married couple at times and many of their interactions tend to come off as UST. Add the fact that they've had some rather tender moments, are far more developed as characters than Davianna, and seem to be shipped by Carole it's understandable why this is.
Moral Event Horizon: What Donatello does with his clone, "Leo", and especially Officer Tony Howard after the latter stumbles upon his lab and experiments.
Nausea Fuel: Frequently. Characters vomit on panel, mangled corpses abound and there's plenty of blood from the second panel on.
Rescued from the Scrappy Heap: Renoir was initially disliked for being exactly like every perverted anime protagonist and their father - Often being called the worst part of the comic in the beginning. However, as he received character development, showed some hidden depths, and improved his mentor/student relationship with Raphael fans of the franchise warmed up to him and he became praised among the fanbase for being an interesting deconstruction of what it would be like to be thrown into the Turtle's world without warning. Something most OC's made by fans often fail to do.
They Wasted a Perfectly Good Character: The major consensous on Davianna so far. Mostly due to not getting much character development outside her relationship with Renoir. Luckily this hasn't caused her to be a scrappy.