Tear Jerker / Pokémon Desolation

• The fact that you're one of the few survivors of the terrorist attack on the ship - and you can only adopt one of the Pokémon who lost their trainers, the others run off and you never find out what happened to them.
• The route where Scarlett sacrifices herself to further Nova's plan of creating an ideal world. And to make things worse, later on it becomes clear her death accomplished nothing.
• Dear God, Tristan's storyline. When you first meet him, he laments how nobody notices him, and later you find out he's supposedly been dead for years. It turns out he's a sentient illusion based on a deceased person, and Darkrai has been using him as a pawn to manipulate you. Distraught over his actions, he defies Darkrai at the cost of his own existence. Just before fading away, he releases all his Pokemon so they'll have a chance at happiness with another trainer - only to find out they're all illusions too, and fading with him. He dies in a state of utter despair.
• It's made very clear over the course of the story that Garret was utterly crushed when the Black Foxes abducted his sister, who he raised from birth. He obviously hates himself for not being there to prevent it, and has given up on finding her or making things better.