- During Chapter 1, the player has to break into a hospital ward in order to investigate EDEN Syndrome. While there, they are confronted with their own body which they were separated from after the Eater attack.
- Agumon and Gabumon were being threatened by hackers before Nokia and the player rescue them. It's only after they're saved that the two reveal that Digimon are creatures from another world. The hackers don't even consider that Digimon are living beings and enslave them for their own, often criminal purposes.
- Almost all the Digimon in EDEN were forced to flee the Digital World. They're basically refugees looking for a safe place and they're being captured by hackers with the Digimon Capture program.
- One sidequest is tracking down someone who's been sending messages on the DigiLine of a Highschool student, who you track down on EDEN. That's not the sad part. The sad part is that the program has merged with a Digimon and completely destroyed its mind. While initially it was to track down the culprit, Kyoko urges you to Mercy Kill the poor thing.
- The ending of the Serial Disapperances in Akibahara. Not only was the woman, Nishino, a friend of Arata, but she was being driven insane by a Wisemon preying on her inadequate feelings. Just when you've nearly gotten through to her, an Eater shows up and she ends up becoming a victim of EDEN Syndrome.
- Another sidequest has you trying to find out more about a mysterious laser that's causing problems in Shinjuku. When you arrive, it turns out to be a digital laser controlled by a Tankmon that was being experimented on by a government as a potential weapon. The Tankmon talks about how it can't live with itself being a weapon, and wants to get away. The sad part is, it's completely willing to cooperate until you receive a message from Matayoshi, which convinces the Tankmon that you're there to take it back to the government and causes it to attack you.
- Oh and don't think this is like other games where innocent people randomly return to full health after a misunderstanding induced fight. Tankmon is NOT fine after the fight and dies wishing it was never born.
- What happened to Yuugo. Not the one you meet in EDEN, the real Yuugo who became the first EDEN Syndrome patient. For 8 years he's been trapped in an Eldritch Abomination and single-handedly kept Eater from going on a rampage.
- Just to make it worse, the protagonist's brave actions manage to push the Reset Button on a lot of bad things, but the part where Yuugo's been in a coma for most of his youth still happens even in the happy ending.
- Yuugo (the A.I. program) attempts to convince Yuuko not to delete it as it cannot exist outside of EDEN. It only wants to keep living. Luckily, Yuuko changes her mind at the end.Yuugo: Please, don't misunderstand. I don't want to hurt you, but... I just don't want to be deleted.
- Beginning of Eden. The second you see an intact Galacta Park, you realize that it's actually the original version of Kowloon. Seeing it makes you realize that a product of love like this eventually gets written over, and replaced by a community of Hackers who just want to ruin it for everyone else.
- The case where Pete/Miko reunites with his master....
- The moment just after the final boss when everything seems to go back to normal. Yuugo returns to his body, the Digimon return back to the Digital World, and Takumi/Ami prepare to head home with their friends... until their body suddenly DISAPPEARS just as Nokia reaches for their hand! She ends up breaking down in the middle of the road when they return to Shibuya.
- At the end of the game Alphamon, who had been acting as Kyoko for the entire game bids the player farewell, calling them their fair "Watson" one last time before leaving. Although the player would go on to meet the real Kyoko later, it's unknown if they'll ever see their trusted friend and savior ever again.
- This also applies to your own Digimon that saved your life by putting you back together. They're going back to the Digital World and it's unclear if you'll ever be reunited.
- Borders on being Fridge Horror, but Yuuko having to look up how friends are supposed to act truly cements how alone she's always been. Of course, the blow is softened by the whole thing being Played for Laughs.
Tear Jerker / Digimon Story: Cyber Sleuth