- While some almost-deaths were pretty sad (an especially sad one is when Quinn received a nasty electric shock), they're basically ruined by being, well, a Disney Death.
- The separation of Cindy and Jenna. One thinks the other is dead, and the other one? Survived, but ended up with amnesia.
- Cindy on the receiving end of abuse of a constantly angry Anonimo. Then, when she saves his life, he repays her for pushing him with a No-Holds-Barred Beatdown with a whip and then left her buried in her Pokeball. And the Heroic BSoD afterwards...
- Probably the saddest event in the story is Jenna's backstory: She had been raised by a trainer named Kim. She got along well with Kim's family (which included Anonimo of all people) and the girls were an unstoppable team. But, then, Kim's parents divorced, Anonimo was going through his Start of Darkness, and Jenna noticed poor Kim stressing out. The saddest part is the accident which both were involved; Jenna survived, but Kim didn't. Overwhelmed with grief, Jenna ran away. During the next few years, Jenna made and lost friends in the wild, had a baby Cyndaquil, Cindy, and then lost her within a week, was captured by Team Vortex, had another baby Cyndaquil, Quinn, but had to hide him and force him to escape without her, not knowing if he'll survive the wild, and just suffering from inadequate food and illness the entire time, trapped in a prison. She's got it hard...
- And then we learn of another side of both Jenna's story and Cindy's. Patch the Feraligatr was originally a Totodile by the name of Snap. His trainer was Anonimo, and the pair were happy, nice characters. However, once Anonimo's father found a magazine about Semi-Legendaries and became interested, things went downhill. Anonimo got interested (not to mention hit puberty), and it starts off with just a desire to catch a Semi. Soon, he gains a crush on a girl that Snap didn't approve of(his future wife, Asesina). Annie's infamous abuse began with just showing Asesina his 'discipline' of the Totodile (by kicking him in the jaw and making him lose a tooth), and kept getting worse and worse. Then, the above-mentioned divorce happened, Kim and Jenna got into the accident, and Snap just wallows in his grief. As a Croconaw, he watches helplessly as Anonimo severely abuses his newly-captured Cyndaquil (Cindy), being too afraid to help. Once the infamous beating took place, his eye gets damaged, he destroys his Pokéball, and he's chased off by the other Pokémon. While he did end up with Lindsay, his outlook on life still soured, and he became the jaded Pokémon we know.
- That one scene... that one scene where Quinn gets a Hope Spot regarding his mother, Jenna, still in the "prison cell" that he was forced to leave her in, only to find said cell empty, and learning she had been moved to another base.
- Ty, whenever the subject of his Malonix virus is brought up. When it comes to that, you can tell how despondent he is, because he has no idea how to fix the problem, or if it can even be fixed without causing harm to those he loves. Killing him would only make the virus transfer itself into a more powerful individual. His general helplessness about the entire thing is even more heartbreaking when you realize it could have been prevented!
- And Cindy feels just as helpless. She even once hurt his feelings by just mentioning it.
- The Quiltuplets leaving their parents, possibly never seeing them again. Cindy's reaction is just heartbreaking, especially since she tends to display anger to cover up sorrow.
- Amber giving a severe chewing out to Sombra, who had let his Superpowered Evil Side nearly kill her and her brother. His reaction is to run away in shame and she storms off the other direction. Because the two had become friends, and were possibly falling in love, the both of them are heartbroken over what had happened.
- Three words, between a pair of quarrelling siblings: "I HATE YOU!!!"
- When Cindy and Ty battle to the death. It's worth shedding a few tears over because they are the Pokémon version of a married couple. Cindy in Blue Fire Frenzy and Malonixed Ty are in control, and they're duking it out until one falls, in front of dozens of horrified onlookers. Malo!Ty wins by punching Cindy in the chest hard enough to cause cardiac arrest.
- Willie getting stabbed, Copper getting shot, Amber getting caught in a rockslide, and Joey receiving a severe head injury while underwater. All done by agents of Team Vortex to get Blaze to go Blue Fire Frenzy.
- What's worse is how they succeed. Sombra and Ivy try to meddle with whatever Dora had planned as the final push for Blaze; unfortunately, the emotionally unstable Blaze doesn't believe them when they try to explain that Dora is a Team Vortex spy. Even when Sombra shuts up (because he senses that something bad's about to happen), Ivy persists, which pushed Blaze over the edge into BFF territory, and he tries to kill her. The tear-jerking part? Ivy and Sombra accidentally lead him to the nearby city, of which the BFF'd Blaze starts destroying. When she's informed that Dora won, Ivy breaks down, and blames herself for the disaster.
- And afterwards, Blaze's depression after realizing that Ivy was right about Dora using him, and the added fear of himself thanks to Blue Fire Frenzy. He's such a sad sap in that scene (compared to his usual characterization), you just want to give him a hug.
- Dynamite's depression after he kills his trainer in a Malonixed State, followed by a distraught Blue Fire Frenzy. There's a throwaway scene where Blaze and Sombra try to comfort him, and the little guy just breaks down...
Tear Jerker / Cindy's Story