Heavy spoilers below; look at your own risk.
- There are a few good tearjerker moments, but probably the most heartbreaking moment comes in episode 19, when Gotsumon tells Ikuto that not only is he a human, but he's the reason why all of the Digimon are dying and the best thing he can do is to kill himself. This after Ikuto has just learned that he's a human in the first place, and having witnessed the deaths of both of his Digimon surrogate parents. Made even worse when you learn that, in a roundabout way, he's actually right. The poor kid's broken scream is probably the most horrifying and heartbreaking sound ever.
- The flashback episodes with Keenan/Ikuto are unbelievably sad, while also being quite scary at the same time. Plus Merukimon/Mercurimon's death. And one man is responsible for all this, and he only gets more evil from there.
- The episodes involving Touma's family are just cruel. He gets a focus episode maybe a quarter of the way in, where an evil Digimon forces him to relive the day his mother died, and he is absolutely heartbreaking. In the flashback, Touma and his mother are on their way to festival that Touma begged to attend, and she was hit by a truck on their way. But it's a Pensieve Flashback, so Touma can't do anything—he screams and yells for his mother to turn back around, and he gets in front of the truck itself and yells for it to stop, there's people here, but nothing. Even the dub did this wonderfully, with Crispin Freeman's screams being almost painful. Near the end, we find out that was only the tip of the iceberg: after Touma's mom died, of course he had to go live with his rich Austrian father. His grandmother, upon first meeting him, tells him point blank: "You are a member of this noble family, yet you also are not" — implying either that he's not good enough because he's illegitimate or because he's half-Japanese. Or both. Then his half-sister, Relena, is born. His stepmom apparently died in childbirth, and poor little Relena is very weak and ill, and just... argh.
- The first time Keenan meets his real parents could count
- BanchoLeomon's sacrifice counts. BanchoLeomon earlier helped the main cast develop greatly and enchance the relationship between their partners,...then he is revealed to have Spencer Damon inside, the Missing Dad who did so much good. And to stop King Drasil from destroying the world, they agree to let Marcus kill him off with King Drasil. This puts Marcus into a Heroic BSoD for a moment, and then,....it turns out in vain.
- Also during that scene, look at Marcus's expression when BanchoLeomon/Spencer pats him on the head and says he's grown. The normally tough, composed, Hot-Blooded gang-typer is crying.
- At the very end, Marcus sees his father, alive and well, approaching his family. Marcus is dazed and he, once again, looks like he's about to cry. Pretty much any scene with Marcus and his father is this.
- Also, Saver's final episode, especially when Ikuto and Falcomon, who have literally been together for their entire lives, have to say goodbye to one another. Yoshino, Touma, and even Satsuma's final moments with their partners are surprisingly touching as well. Subverted when Masaru decides to Take a Third Option and go to the Digital World with Agumon.
- Everything involving Biyomon. He just wants to protect Kristy but can't because there's a danger that he'll be overcome with human emotions and go feral like the other Digimon that had come before him, and what makes it worse is that it happens and they're forced to turn him back into a Digi Egg.
- Of all the Digimon to die in Savers, ElDradimon/ElDoradimon has one of the most cruel and tragic deaths. When ElDradimon—a colossal, peaceful tortoise that carries a thriving Digimon city on its back—comes under siege from Kurata's minions, the heroes spend multiple episodes trying their best to defend it on all fronts. Unfortunately, they can do nothing but watch in shock and despair when Kurata's Gizumon form a gigantic javelin that drops from the sky and drills slowly and painfully through ElDradimon until it and its Digi Egg completely disintegrate.
- Made sadder when earlier, Baromon (the city's mayor) is killed by a Gizumon XT and his dying words are that the heroes keep ElDoradimon safe.
