To preface, ultimately perhaps the biggest tearjerker in The Nutcracker in 3D is its usage of Nazi and Holocaust imagery, and the implications of living things being systematically murdered and burned up in a giant crematoria. The film's family-friendly musical structure is extremely jarring in juxtaposition, and the dark themes are coupled with images of young children in black-and-white who are screaming and sobbing hysterically over the destruction.
- A live shark is electrocuted and killed on-screen.
- Mary finds Gielgud lying on the floor after being knocked down. Realizing that the other toys and her little brother have all been taken by force to the Smoke Factory, Mary sobs in Gielgud's arms while he comforts her.
- Mary's father reveals (via conversation with Uncle Albert) that his stuffy attitude and annoyance towards childish things is the end result of him having lost his favourite childhood toy, a pebble that he found on the ground and had pretended was magical. The father then cries and realizes that he has been unfairly rude to Mary, who is just a little girl.
- Max breaks down sobbing upon the realization that his boyhood hobby of breaking his sister's toys has actually been harming living souls. Not only are the dolls in the film all alive, but Max is also witness to them being snatched from the hands of crying, screaming children and burned to death in a massive crematorium.
- The Rat King, Mary discovers, is actually very self-critical and believes himself to ultimately be stupid and beneath human beings. When Mary tries to compliment him, he doesn't understand that she feels sorry for him and instead perceives her compliment as patronizing. His attitude is explained when it's seen that most of the humans and living toys in N.C.'s world consider the Rat People to be dirty, cowardly and uneducated.
- There is a near-death scene where Mary believes that N.C. is dead. She drapes her coat over his body, sobs and declares that she loves him, holding his hand while kneeling in the middle of the Smoke Factory where the toys are being burned up.
- When Mary tries to explain to her parents the urgency of saving N.C. and why she is so upset, they scold her and her father threatens to take the nutcracker doll away from her; this leads Mary to run upstairs and hide in the attic because "I don't want anyone to see me cry."
