* The whole endgame, from [[spoiler:Issun's departure, to the ghosts of the Celestials telling how they died, to Waka's tale, to Ammy's HopeSpot halfway through the final boss battle.]]
* [[spoiler:Tobi]]'s death. The little guy was helping you all along and then gives his life up to help Ammy reach the boss. He even left a small flower where he faded. Poor [[spoiler:Scrap]].
** Which makes it all the worse when you realize his final words are how he wishes he could offer you a flower in congratulations and that this is the first time he's enjoyed himself so much. He then proceeds to turn himself into a flower and, even though all enemies do that when they die in this game, it hits home that much harder because his final act becomes the fulfillment of his final desire. What's worse is that a lot of players don't even realize this and will simply continue their quest, ignoring his little flower once he is gone.
*** Well, ''some'' players [[PetTheDog appreciate]] [[spoiler: Tobi]] and what becomes of him.
* Just Waka's tale in general. [[spoiler:Although he does not outright state it, he hints he is the last of the Moon Tribe. He also was the reason that Nippon has demons in the first place. His whole TricksterArchetype is based on the fact that he doesn't want to let anyone get hurt. And when he saves Ammy from Yami at the apparent [[HeroicSacrifice loss of his own life]]...]]
** Well, he isn't really the last, there's also Kaguya, who goes off in a rocket and is never seen again. Which is a TearJerker in its own right since she flies off in the hope of finding out who she is and where she comes from. If Waka and [[spoiler: the Celestials]] can be believed, then [[spoiler: she will be entirely alone and possibly with no way to leave.]]
* After your adventures inside the Dragon Palace, the dragon orb shows you a vision of the [[spoiler: REAL Rao being attacked by the demon Ninetails]]. Cue epic music as Issun rushes you to where the vision had shown you. Once there, the ghost of the [[spoiler:real Rao]] leads you to a secret tunnel. So when you go into the secret tunnel, you find a decayed corpse. Guess whose it is. This is one PlayerPunch guaranteed to leave you winded.
* You see? Nobody remembers [[spoiler:Queen Himiko]], not even the people in the game itself. Both her and Ammy knew that she had to die for her plan to work from the very beginning yet none of them mentioned it, her sacrifice is quite tear jerking. The way she manages to linger on in this world for just one more moment in order to finally determine the location of [[spoiler:Oni Island]] for this one sunset was also rather sad. The saddest part of this is the fact that the ''Emperor'' never talks about her.
*** Even before that, her entire situation was incredibly poignant. She did all that she could by praying constantly, but until Amaterasu happened upon Sei-an, it was doing absolutely nothing. Her people were crying to her out of anger and desperation and she could do almost nothing to help. When Issun calls her out on doing nothing to help her people, she understandably breaks down sobbing.
* Kaguya going back to the moon.
** Made worse when you find out that [[spoiler: there's no one left on the moon due to a cataclysm. After all, that's why Waka left.]]
** She does promise to come back, but since she never returns, its left open if she survived the flight or if her rocket even has enough power to allow her return to begin with.
* Issun [[spoiler:imploring the people of Nippon to pray for Amaterasu's safety and give her their strength]] in the final battle ''never'' fails to turn my waterworks on.
* Going [[spoiler:back in time]] and eventually watching as [[spoiler:Shiranui]] dies.
* "[[AwardBaitSong Reset (Thank You)]]", which plays during Ammy's DarkestHour.
** The song becomes even more poignant when you remember that this is one of the last games Clover made before being shut down.
* The one part where you are eaten by a dragon, and you tamper its insides so much that ''you end up killing it by accident'', and it's not even in the least bit played for laughs or awesomeness. You just feel bad for doing it.
** The song that plays as it falls into the depths really doesn't help. It gives you the feeling that you just destroyed something beautiful and majestic. Even the way the cutscene is shot is emphasizing on it as it has Amaterasu quietly watching as the dragon slowly falls deeper and deeper until it disappears in the darkness, it's body totally limp. Even if ignoring the text of Issun between it, Amaterasu spends almost a minute just quietly looking on.
** And then you go tell Queen Otohime, where Issun breaks the news in the worst possible way.
** Let's not forget TheReveal that this dragon [[spoiler: had been the king]] all along, making Issun breaking it to Queen Otohime even more devastating.
** There's also the fact that Queen Otohime [[spoiler:was actually ''pregnant'' during that time. In the credits, you even see her holding her baby. That's right. You've just made a child fatherless.]]
* The music that plays when you're in a cursed area, particularly Shinshu Field when you hear it for the first time. That flute...
* During your search for the Canine Warriors, you return to Kamiki Village and find that Mushi's dog, Hayabusa, is actually one of the warriors, and that her real name is Chu. The real Hayabusa died along with Mushi's father when they were attacked by monsters in the woods. Chu found them, but was too late. With her dying breath, Hayabusa predicted that Mushi would be killed by an evil arrow from the sky on the night of the full moon. No one noticed the switch because they were the same breed. Because of her promise to Hayabusa, Chu even does so much as to refuse to return to Princess Fuse. Thankfully, the Loyalty Orb is given to Ammy, and Chu is able to fulfill her promise. Canine Warrior of Loyalty indeed.
** Mushi later reveals that he knew all along that Chu wasn't Hayabusa, because he knew that Hayabusa would've died to protect his father instead of running.
* One assumes that Amaterasu was always there to protect her people, but in Peony's time Nippon was known as "a land of great sadness", so vulnerable that Peony ''crossed the ocean'' to help it.