Tear Jerker / God Eater 3

• The state of Earth in general. Not only are Aragami still ravaging the Earth, the appearance of the Ashlands has made the whole situation even worse. Orphaned children are being forcibly turned into AGEs and used as disposable tools, this going so far that most Ports don't even see them as human anymore.
• Early in the game, Hugo pleads for the Protagonist to live after they took the hit from Anubis aimed at Phym just before they lose consciousness. Granted, the Protagonist gets better thanks to Phym's Healing Hands, but imagine this: the Protagonist is practically the closest friend/surrogate family Hugo has, having spent the majority of their lives together...and suddenly said closest friend/family nearly dies in front of him. It is also one of a few times he is visibly shaken after appearing calm and collected most of the time.
• There is an event between Hugo and the Protagonist in late Rank 6 following Gleipnir's declaration to sacrifice AGEs to empower Odin and Hilda's subsequent defiance against it by ordering the Chrysanthemum to make an escape instead of sacrificing anyone under her care. In the event, Hugo expresses how he did not expect anyone in Chrysanthemum would side with them in the matter despite the fact that they have been nothing but supporting towards the Hounds throughout the game, and how spending so much time as AGE has filled him with negativity and promptly wondering if Zeke and Lulu feel the same way. This also shows that despite his kindness and determination to protect his loved ones, he did not go through the experience of being an AGE completely unscathed. Judging from the Protagonist's reaction, it is likely they feel the same way or at least understand where he is coming from with that sentiment.
• In late Rank 6 there is a conversation between Phym and the Protagonist which shows just how much Phym has grown as a person - and how heavily the ongoing war is affecting her.
  Phym: I want to make everybody happy. But I don't know how to do that. Even though I'm studying so much.
• In the last cutscene before the final battle against Odin, we hear what Phym wrote in her letter to the crew of the Chrysanthemum. The whole situation is already heartbreaking in itself, but having to listen to Phym saying goodbye while the Hounds desperately fight their way to Odin in order to save her is just heart-wrenching. Then Phym addresses the Protagonist...
• Ein's deteriorating condition at the end of Claire's Character Episode. Having been a God Eater for so long (keep in mind Ein was quite literally born as one), he's finally reached the point where Phym instantly senses what's happening inside his body and says that "[Ein]'s Aragami wants out." Having known Ein for so long, who has been with fans since the first installment, it's heart rending to hear that he's slowly approaching the last vestiges of his life. And by his own account, he has six months left in him.
• At the end of Hugo and Zeke's Character Episodes, the former explains how the Cataclysm that created the Ashlands and made Northern Europe (and possibly the rest of the world) into a hellhole came to be. Three people came together for an experiment of unknown purpose, during which an accident occurred. Said accident caused the cataclysm, and as a result, the three scientists were branded as criminals in the eyes of the public. One of those people was Soma. It's little wonder why he changed his name to Ein if everyone now hates his guts.
• Ein's Character Episode. All of it.
  • The opening has Ein falling comatose, unable to resist the Aragami inside him any longer.
  • Afterwards, Hugo decided to make announcement to everyone about Ein being Soma Schicksal - who is at this point known by them all as one of the three people responsible for the Calamity. Naturally, everyone was rather shaken upon learning this, but chose to help Ein anyway.
  • Before the Calamity, Soma actually tried to persuade Dr. Heidenstam and Dr. Kwon to postpone the Project Ragnarok for at least two years because he found fundamental flaw in their final simulation result that necessitates overhaul in the core system that would endanger everyone involved if left untended. His collaborators didn't listen and went ahead with the testing, which soon Gone Horribly Wrong.
  • Soma's Skyward Scream as he hopelessly watched that nothing was left from the Fenrir HQ - especially the survivors as they have all been turned to ash. The sheer horror and despair throughout the scene is palpable.
  • Upon receiving call from Lindow and an update on the situation in the Far East Branch, Soma blames the whole mess on himself and vows to fix the mess. In what doubles as Heartwarming Moment, Lindow didn't blame him at all, instead he encouraged Soma to keep going and he will keep the Far East Branch safe in his place. Soma changed his name to Ein afterwards and vows to uphold that name as long as his job is not done.
  • The biggest kicker of all, however, just of how much the incident crushed the dreams behind the Project Ragnarok: to eliminate all Aragami once for all and finally free humanity. What they got instead was that everything humanity had fought so hard to protect and built for crushed in the presence of the Ash Storm, forcing them into corner more than before.
  • Despite being the one responsible behind Soma's deteriorating condition, in the end the Aragami inside him only wants to help him by granting him a Mercy Kill, having been unable to do anything for Soma for years and believing it is the only thing he can do. Even before this, Phym stated from time to time that the Aragami inside him "is crying", which makes one wonder just how hopeless he feels.