Even for an animated TMNT film, it still has its scary moments.
- The first appearance of the Stone Generals has them slightly moving in a creepy manner.
- The opening battle between the armies and the soon-to-be Stone Generals. It is terrifying and violent to watch.
- Winters helplessly witnessing his siblings being turned to stone and himself being cursed to live forever without his siblings. By the time the film actually starts, he quite understandably has become The Atoner.
- One of the mooks being hit and knocked out cold by the Nightwatcher's chains. Any harder and he would've been dead.
- When Santino's men in the South American jungle get taken out, Leo reveals himself to him. Santino pulls out a machete and the scene cuts with the sounds of his screams and birds flying out of the trees, implying that Leo killed him.
- One of the 13 monsters, a gargoyle, perched atop a building devouring a bird. You can still hear the bird screeching inside the creature's mouth and all the monster does is swallow the bird whole, belch and smile evilly at the camera.
- The DVD Commentary reveals that the bird was supposed to be heard inside the stomach of the gargoyle, still alive, and the belch was added in post to avoid a PG-13 rating.
- The first appearance of the Yeti monster complete with its loud roars can be unsettling, and this is after it was toned down.
- The rest of the 13 monsters being captured and taken in by the Foot and the Stone Generals. Each more terrifying than the last.
- Even more terrifying is the fact that the monsters were inspired and modeled after crypt-zoological creatures.
- Raphael losing his temper and almost killing Leonardo in their rooftop fight. This is the closest the audience has ever seen Raphael come to nearly killing his own brother and getting lost in his anger.
- The close up shots of Leonardo and Raphael's faces just before their second rooftop showdown.
- Their exchanges before the battle: "Don't do this, Raph." "I'm done taking orders."
- The thunder clapping during the emotional sibling fight between Raphael and Leonardo doesn't help either.
- The laugh Raphael makes just before taking out his sai, ready to fight his own brother can be a bit unnerving. Especially considering what happens next.
- Leonardo's blood-curdling screams as he's captured by the Foot and the Stone Generals.
- The restaurant cook discovering the Jersey Devil monster in his freezer and screaming loudly.
