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Tear Jerker: Shin Megami Tensei IV
Issachar's death. Especially Jonathan's desperate attempt to find some way to save him, and Issachar's final words begging Flynn to become powerful enough to change the world.
If you try to use chat skills against this boss, you'll learn◊ in the most heartbreaking way that The Dev Team Thinks of Everything. One of the few cases, along with the Isabeau example below, where using conversation skills on the boss is not funny.
No matter what you say to him, Issachar gets punched in the soul very badly. Say you still consider yourself a Casualry? He killed Kiccigiorgi and turned himself into a demon for nothing. Suppose you say you're a Luxuror? His best friend essentially is telling him to rot in hell.
When you get to the part of the game where you get to choose to go along with The White's plan or go against it, if you decide to reject their plan, you have to fight The White version of Issachar. When you defeat him, he asks the hero why he never saves him. It's striking if you had empathy for Issachar and felt bad about him dying earlier in the game. The White have some nerve to guilt-trip you like that.
Being forced to kill Isabeau in the Law and Chaos paths. Many players consider this one of the most emotionally powerful moments in the entire game.
In the Law and Chaos paths, Isabeau kills herself by slitting her own throat. Doubles as Nightmare Fuel when you realize that she would rather kill herself than follow you.
Or conversely, a Crowning Moment of Heartwarming, albeit a very morose one, since her stated reason for slitting her own throat is so that you aren't burdened with the guilt of having killed her with your own hands.
Using the Trade or Fundraise commands on bosses usually ends up with hilarious results. Not so in this fight: Isabeau complies to your demands because she wants to honor your old friendship. Yes, while you two fight to death.
During battle, Isabeau will talk to you at two points. The answers that debuff or take way Press Turns from the enemy side are the ones that hurt her the most. Geez, talk about rewarding cruelty...
On a similar tack, when you go neutral and are found by Isabeau again, her reaction to you being alive and her not being alone anymore is going to get you right there.
On the same route, you can actually find the final volume of Rose of Versailles she's been looking for. Her reaction to getting to read it is priceless.
If you decide to go for the Bad Ending and accept The White's plea to end all existance by overloading the Yamato reactor. Burroughs still assists as Mission Control, but her lines take a notably sadder tone as she notes this is probably where you part ways. The way she says "Congratulations... on completing your objective." once you finish is heart-wrenching.
There's also the matter of destroying existence in the first place, which the White wish to achieve because they've become so jaded and tired of the whole Law-Neutral-Chaos conflict.
One Challenge Quest has you taking a picture of a ruined bar in Shinjuku for an elderly woman who says outright she doesn't have much longer to live. When you give her the picture, she reveals the reason that the bar was so close to her. She owned the bar and ran it with her daughter. Her daughter was murdered and eaten when the demon invasion first began 25 years ago.
It's more hard-hitting if you pursue the Law path or the Nothingness path, because you're hastening her death even faster.
Watching Walter and Jonathan's friendship break apart as their Law and Chaos alignments come into direct conflict. Unlike most games in the series, in which the Law and Chaos heroes butt heads pretty much from the beginning, these two were True Companions, and watching them torn apart by some cosmic war is heartwrenching.
As an example, the scene in Tsukiji Hongwanji where Jonathan tries to carry out the Monastary's orders to kill the Black Samurai / Yuriko / Lilith, Walter blocks Jonathan's blade because he stands for Lilith's vision of a world ruled by Chaos, and all Isabeau can do is watch because she doesn't want to side with one of them and oppose the other.
On a similar note, seeing Walter being reduced to nothing but a grotesque arm-fetus-thing for Lucifer is really sad, especially on the Neutral route, where he's reluctant to even fight you.
It's just as horrible in either Law or Chaos to hear them again, just once, as either Lucifer or Merkabah are dying. Jonathan just screams in anguish, asking what is it that you want, and Walter just crushingly invokes Chaos' philosophy; if he lost, then it means you're the strongest anyway. And then you either allow Merkabah to press the remote or return to see East Mikado in flames. Hammers down just how painful it is to change or to preserve the world.
In another similar note, the events at both the Blasted Tokyo and Infernal Tokyo are even more disheartening because that is the last time you get to work together with the both of them before the cosmic war completely destroys their friendship and no matter which path you take you have to face off against one, the other, or both in the endings.
Kiyoharu may have been a pitiable figure, but the Ancient of Days stomping on his faith and shattering it with just a few exchanges was just uncalled for.
In Infernal Tokyo, Kenji successully had the angels killed, stopping a nuclear holocaust, and prevented the Cocoon from leaving. However, they were unable to crack it open soon enough, and God's chosen within all died. A Demonoid in Infernal Tokyo's Shinjuku National Park laments his perfect sense of smell, as it reminds him of the smell of the scene when the Cocoon was opened and he found his daughter rotting inside.
In the Law route, you can continue to conduct Challenge Quests in Tokyo, even knowing that you'll be wiping the entire prefecture from existence very soon, thereby rendering your acts of generosity pointless. All those quests involving the futures of their clients and/or Tokyo? Congrats, you're shooting the shaggy dog.
Blasted Tokyo, which you arrive at after opening the gate to the Expanse, is terrible. The entire city has been bombarded to ruins by the forces of Law and the remnants of humanity have been surviving on stockpiled food for the past 25 years, unable to go outside because Pluto's poison and the demons will result in very quick deaths. Shibuya within Blasted Tokyo is just gruesome; everyone in the shelter is dead, reduced to ghosts who are bound to the place.