- Charmcaster's crying moments in "Where the Magic Happens", "The Enemy of my Frenemy", AND "Couples Retreat". Charmcaster's character arc was depressing to a ludicrous degree, especially since it was left unfinished and she's left alone.
- The ultimate fate of Kwarrel, the prisoner who taught Kevin to control his anger.
- In-universe, Kevin attacking Gwen and then holding off for what they had, in his words causes her to cry for the first time in the series.
- "Eye of the Beholder" really shows how bad Ben and Julie's relationship has gotten. Ben refuses to find Ship out of sheer pettiness because they broke up. Remember, this is the series where Ben's Chronic Hero Syndrome has been cranked Up to Eleven and yet he absolutely refuses to help Julie. Amicable Exes, they are not. Of course after they well and truly break up, Ben wants to get back together with her but the damage has been done. Even when they get back together at the end of the episode, it's undercut by the fact that as of Omniverse, Ben and Julie really did break up and Ben didn't even realize she had found someone else.
- The fate of Victor and Elena Validus. Turns out Victor died offscreen in an experiment and that the Hive used Elena as a secondary Queen to survive, making her believe everything they do is just what she wants them to do and she's in control. Ultimately, unable to allow Ben's death, she manages to regain control and kill herself along with the Queen. What makes it even more of a Tear Jerker is that The Stinger reveals it was in vain as the Hive survived.
- Less of one now—Turns out Elena somehow survived too and is even crazier. She brought two buildings to life to try and kill Kevin when he got too close to figuring out she was impersonating Julie.
- Less of one or MORE of one? Death is probably preferable to madness.
- "Prisoner 775", everything about the title character in general. He was exiled from his planet for trying to overthrow a dictator, loses his family and when he gets to Earth, he is almost immediately called a terrorist and thrown into what can be best described as a POW camp for aliens. Don't worry it only happens for four to five... decades. The worst part is when he breaks down at the end and begs Ben to put him out of his misery and let him rejoin his dead family. As if that wasn't bad enough, the one responsible for his torment, Commander Rozum, never suffers any consequences for his actions aside from losing the respect of a few people (which he could care less).
- In "Ultimate Sacrifice" Ben was going to die willingly so that some of his Ultimate forms could escape the Ultimatrix and be free.
- Jennifer Nocturne's backstory in "To Catch A Falling Star".
- In "The Ultimate Enemy", Old George's death.
Tearjerker / Ben 10: Ultimate Alien