- Rarity's breakdown in episode 14.
- Applebloom almost going through the Despair Event Horizon, after her plan to stop Equestria's enemies fails miserably.
- Celestia realizing how badly the war is going and deciding to personally intervene, before finally giving Luna a chance to prove herself. note The whole scene, has a surprisingly depressing and serious atmosphere around it.
- Seeing Fluttershy have to come to terms with the fact that her fear has caused the death of an innocent creature is quite a gut punch, especially since it comes right after a comedy scene.
- Episode 23 is a tragic episode for the Apple family. They receive a message saying that the Apple siblings' mom died. The Apple siblings' mom abandoned the family when Applejack was only 10 years old and that she said that she would only return if there weren't anymore apples, which resulted in Applejack's deluding herself into thinking she was farming mangoes instead of apples. According to Granny Smith, she wasn't referring to the fruit. After Applebloom was born, she felt like she was set up, as Granny Smith named their mom 'General Builder' and Celestia took Applebloom to a military academy to become a general.
Tear Jerker / Scootertrix the Abridged