- Very early in the game, after your partner leaves Goomy behind in the dungeon, your partner starts to wonder if they're annoying. They ask you and regardless of what you say, they will become upset and they will not talk to you for a bit. The next day, they will not ask you to walk to school with them because they don't want to be irritating.
- Budew went to the Beedrill and Combee to gather Honey because her mother was sick and she hoped it would cure her illness.
- Telling your partner you have to leave Serene Village is pretty heartbreaking. Your partner understands that you want to protect everyone, but they clearly do not want to lose the only friend they have. Subverted though, when they decide to come along with you anyway.
- Before you leave Serene Village, with your partner, you are stopped by Deerling, Goomy, Espurr, Shelmet, and even PANCHAM. They all want to say their goodbyes. If that's not sad enough, its revealed that Espurr told the adults and they accept the fact that you are leaving the town. All of the major characters in the town leave you heartfelt letters, including ones from Carracosta and Nuzleaf.
- Someone who is closest to a father figure as it comes, turns out to be manipulating you to do what he wants the whole time. Of course we then find out that he was under the control of Dark Matter. But he still can't bring himself to show his face to you, whether if you forgive him or not.
- The ending has yet another sad goodbye scene. This time, you're the one left heartbroken, as you watch your partner fade away.
- And then the credits roll with super-dramatic music as you stand under the big tree alone, crying over your partner's absence.
- If you take Mew to Serene Village before Purifying Cave, everyone will comment on your new friend but what really makes it sad is that Carracosta accidentally mistakes him for your Partner. And when he realizes he isn't he shakes his head sadly saying that he's seeing things. He really misses his kid.
- Mawile and the Legendary Beasts' Heroic Sacrifice. The escape point is mere inches from them, but they choose to stay behind and fight against hopeless odds just so you and the Partner have a chance to escape. Ampharos is absolutely crushed that his lifelong friend and partner is gone, which explains why he's so pissed when you confront Nuzleaf again. Especially poignant as, since Mawile was no doubt defeated by the Voidlands Shades, there was no guarantee that her soul would return to her body once Dark Matter's petrification was undone.
- Have a Legendary Pokemon as one of your favorites? That won't save them from being turned into stone and essentially dying which can be dispiriting if they are among those that are killed on screen. The Lati twins may have the worst death; a close look at the way their statue's arms are spread out and angled implies that the two siblings were trying to hug each other as they die, or even trying to push each other out of the way of the villain's attack only for both of them to become petrified. After being separated during the events of the first game, it wouldn't be a stretch that they were completely desperate to protect each other and not lose each other again.
Tear Jerker / Pokémon Super Mystery Dungeon