- The kids running to embrace their grandfather after he defeats Snyder.
- The reunion between the entire family at the end, where their dad calls them heroes and uses their ninja nicknames that he's been set against the entire movie.
- Colt and Rocky's classmates are all cheering for them during their basketball match against the bullies.
- Knuckle Up
- It's nice to see how everyone in the pizza parlor averts being Apathetic Citizens by showing horror and disgust when J.J. throws Jo to the ground and then cheers for the brothers standing up to them. Granted, it does get the boys told off for showing off, but it's still kind of touching.
- The ending of Knuckle Up has the brothers learn a good lesson about being content with accomplishing heroic deeds without needing to get credit for them. The proud smile on their grandfather's face really sells the scene.
- In Kick Back, after a bully calls Rocky a "four-eyed beast", Tum-Tum angrily says only he can call Rocky that.
- Tum-Tum feeling homesick for his parents in Kick Back, which is followed by a scene showing them talking about the boys, is touching.
- Rocky and Miyo are both are initially embarrassed to put their reading glasses on in front of each other. Once they do, they smile about it and lean in for a kiss before his brothers interrupt them.
Heartwarming / 3 Ninjas