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Tear Jerker: Final Fantasy XIV
The imperial strike on the Waking Sands. You just defeated Titan, one of the most awesome bosses in the game. You've been congratulated, now you just need to return to the Waking Sands. So you do... and find rooms filled with corpses, and none of the main Scions are to be found. The only one left is the sylph who followed you from Gridania. She passes on a message from Minfilia, then dies. And you learn through the Echo that she could have survived; she was told to stay out of sight and pass on the message, but was unable to stop herself from trying to protect Minfilia. She is kicked into a wall so hard, she bounces off it.
Just when you think it's over, a few missions later, you're required to help clean up the mess. This means piling up some corpses into a wagon. Including the sylph's. Her's takes less time to pick up because she's so light. And the local church insists that you take her home for her burial rites, so you have to break the news to the other sylphs...
The End of an Era cinematic. Even with no context at all, it will make you tear up thanks to the score.
The "Trusted" (Rank 4) Reputation mission for the Amal'jaa. Loonh Gah infiltrates the Flamefang encampment for revenge and in hopes of finding her mother, who was taken as a slave in the same incident that nearly killed Loonh. And you find her mom... in a cage, cradling a rock, which she calls Loonh, and wants to protect... so she can offer her own child to Ifrit.
When you turn in "The Voyage of the Goobbue", an otherwise standard Mass Monster Slaughter Sidequest, Barryn tells you about how the goobbue had basically meandered everywhere after the Calamity drove it from its home, causing it to also pick up plant life from everywhere. He lists the places it'd been and the seeds it'd picked up, barely stopping short of a Tannhäuser Gate reference.
Barryn: To wander is a dream and a nightmare.
All you've seen Alisaie been is sharp-tongued and hot-headed from when you first meet her up to the Binding Coil quest line. That image is shattered at the end of the Second Coil where the aetherial shade of Louisoix appears, nearly kills her, then revealing that he's been tempered by Bahamut. Before he disappears from your sight, he threatens to kill her and you if you two try to go in there again to disable the rest of the coils. All of that within a matter of minutes. Alisaie has to accept the fact that her quest to go avenge her beloved grandfather is being stopped by the man himself and that the only way she could save him is to kill him. For the first time, you see Alisaie break out in tears, heartbroken.
The story involving the quest "Corpse Groom", and the Tam-Tara Deepcrofts (Normal and Hard). Way back when you were a newbie (Or returning back to Eorzea after getting flung into the future by Louisoix), you met another adventuring party, that actually was looking up to you due to your early exploits in the realm. A bit later, the party's gladiator, Avere dies in Tam-Tara trying to clear it due to party miscommunication. Said tank was the lover to conjurer in the party named Edda, who was blamed for his death by her fellow party members. One of the party members, Liavinne, went on to join the Scions of the Seventh Dawn, and sadly was killed in Livia's assault on the Waking Sands during the main story. Flash forward to Patch 2.3, and Edda resurfaces, claiming that she's getting married to her dead lover Avere, and invited Liavinne and Paiyo Reiyo of her former party. The Torn Folios you can read in the dungeon make it clear Edda's hit the Despair Event Horizon like a freight train and ploughed straight into Crazytown, and worse, a Moral Event Horizon. At the end of Tam-Tara Deepcroft (Hard), she ends up falling off the platform the battle takes place on into a very deep pit, her clothing igniting by passing too close to some candles she walked through.
To top it off, not a single one of your party member cheers at the end of completing it, as normally happens after clearing a dungeon. Instead, your character just looks on solemnly and closes their eyes in regret that it ended that way.
Towards the end of the 2.3 storyline, Sultana Nanamo and General Raubahn discuss recent events including Teledji Adeledji's uprising and plan to claim Omega Weapon. Raubhan notes that thanks to insufficient evidence and rampant Loophole Abuse, nothing can be done to convict Teledji of any crime. Railing against the corruption of the rule of law and her own powerlessness to do anything about it despite supposedly being head of state, Nanamo breaks down and runs into Raubhan's arms crying. All he can do is reassure her that it's not over yet, but it's doubtful how much even he believes it.