The entirety of the game's "Normal Route" is one long tear-jerker. Chizuru, separated from the Shinsengumi during the battle of Toba-Fushimi, follows their progress across the country trying to catch up with them, and arrives at each location only to learn that the Shinsengumi have already withdrawn from the area and that another of the men she cared about and admired is now dead. She clings to hope up until she reaches Ezo and hears of Hijikata's death, at which point, finding a discarded Shinsengumi banner at the side of the road, she breaks down weeping.
Oh my God. My breath catches in my throat, and I feel a rush of blood through my body, warmth starting in the pit of my stomach and spreading through my chest and up to my face. It’s the kind of adrenaline you get in a moment of shock, where the body floods the system to be ready for anything, fight or flight. I am stunned. There are no words for this — I never expected this to happen. I never thought something like this would happen. Not to Kondou, not to anyone I knew. Even when everything was at its worst, even when we were under fire from artillery shells as we desperately attempted to evacuate Kyoto, I never thought Kondou or anyone else would die. ... All that up there? All those feelings, those physical reactions, that adrenaline? That was me in real life. Oh my God. THIS GAME.
Unrequited love endings are nothing to scoff at, in a classic Hakuouki fashion. All of them either have the person you've been following for all this time just shrug you off to protect you, tell you to leave them with maybe a couple of words... Or they just die in a bittersweet fashion without you even being present.
Special mention goes to Okita's in Kyoto Winds: Rather than any of the above, it basically has their relationship destroyed to the point where Okita threatens to kill Chizuru if she comes near him again. Unlike before, this time he doesn't seem to be joking.
Although it has yet to get a localization, Tsukikage no Shou doesn't disappoint on the angsty side of things.
It also gives us some heartbreaking insight into what Sannan's ruse in his route actually had him do. Chizuru is so horrendously broken and hopeless (and who wouldn't be if the person they had faith in turned out to actually be evil and said person killed their comrade and friend in front of them, only to then capture them to be experimented on by their father and brother) that she actually is going to starve herself. That's bad enough, but Sannan isn't actually evil, just faking, and is having to watch Chizuru waste away with the knowledge that if she had the tools available she would have probably already killed herself. All without breaking character. And the only reason Chizuru continues to move forward past this scene? That is due to her own spite for Sannan, and her desire to see the Shinsengumi again. Sannan mentions that as long as her hatred for him is what keeps her alive, it's fine, which would double as heartwarming if only the circumstances weren't so grim.
Yamazaki shielding Hijikata from Kazama's sword with his own body, and his urgent speech to Hijikata while grievously wounded: "What are you doing, Vice-Commander? You're the leader and we're your subordinates. You can always replace your subordinates... But if we lose our leader, it's all over..."
The aftermath of the battle with Kodo in Sendai - just when it seems like for once everything will be all right, Heisuke and Sannan both collapse, their last energy burned up from using their Fury powers. All Hijikata can do is clasp both their hands as they say their final farewells and crumble to dust.
His bad ending at the end of Kyoto Winds has Kazama killing Hijikata in a way Chizuru describes as "the most horrific thing" she's ever witnessed.
Okita's Route
In Okita's final bad ending, he takes a mortal blow protecting Chizuru from Kaoru, and dies in her arms, regretfully lamenting that he's leaving her alone and asking her to tell him again that she loves him. To make matters even worse, this one has its own unique gallery image.
His last bad ending having its unique CG means that, if you want to get that trophy for getting all of Souji's CGs, you have to get his bad end in a route that has enough pain and tears when you're taking the right choices.
Okita's route in the prequel is this as it gives a brief glimpse into his childhood and justifies his strained relationship with Hijikata. All Okita wants is to be useful to Kondou. Kondou (and especially Hijikata) would rather he go back to the safety of Edo and not stain his hands with the Roshigumi. All of Okita's efforts to be accepted basically boil down to one decision: does he want to stay Kondou's kid brother and keep him happy or does he want to become the Shinsengumi's sword which would help achieve Kondou's goals but hurt Kondou's image of him. He chooses the latter.
For that matter, anytime Kondou praises Hijikata in front of Souji.
Kazama's Route
Like the "Normal Route", Chizuru spends Kazama's route trying to catch up to the Shinsengumi after they deal with her father. Like the "Normal Route", they always arrive after the Shinsengumi have left, and always hear that someone else is dead or missing. The difference comes when Chizuru tries to rush to the Imperial-occupied Aizu Castle, and Kazama confronts her over being reckless; in the ensuing argument, Chizuru is forced to admit that the Shinsengumi aren't just going to lose, they'll be painted as villains...which only strengthens her resolve to get there, so she can honor them by witnessing their final moments. On the one hand, it's happier than the Normal Route because at least she's made her peace ahead of time. On the other, her vow brings the waterworks in a different way.
Hearing about Harada's death. Chizuru meets Shiranui, who is unusually solemn as he asks her if she remembers Harada. Her breath catches as she realizes there's only one reason he would be asking that in that tone of voice—and sure enough, Shiranui quietly says he's dead. He describes how they struck up an alliance to fight Kodo's Furiesand how excited Harada was to get to battle alongside him. Then he finishes with this:
Shiranui: Maybe it's me. Maybe I'm just bad luck, since everyone I fight alongside ends up dead soon after.
Chizuru's reaction when they yet again miss the Shinsengumi at Sendai. At first, she tries not to cry because she doesn't think her own pain compares to theirs. Kazama, in a rare moment of gentleness, tells her that just because she's not good with a sword doesn't mean she's not fighting too, or that she doesn't have her own demons to slay. She still tries not to cry because she doesn't want to lose sight of the Shinsengumi's ships. Then Kazama turns around to give her some privacy and she just breaks, pressing her face into his back and weeping bitterly.
Souma's Route
In most routes aside from his own, Hijikata is killed offscreen (reflecting the real-life Hijikata's death during the final conflict of the Boshin War). In Souma's route in Edo Blossoms, we actually get to see his final moments, in which he passes the Makoto Flag to Souma, essentially making him the new commander of the Shinsengumi.
Inoue is carrying a vial of the water of life. He tries to take it after he's mortally injured, but one of the soldiers ganging up on him steps on his hand and crushes the vial
It only gets worse from there. Notably, we have the deaths of Heisuke and Okita. First is Heisuke. As he's dying, asks Saito if he was good for something after all with a smile on his face. The normally stoic Saito Hajime clutches Heisuke in his arms as he's turning to dust with a sweet voice that Heisuke didn't only do good, he saved him.
But by far the absolute mother of all heartbreaking, horrible things in that same damned scene is Okita's death. Even if you thought Okita was a bit of a mixed bag, the Saito and Okita friendship was one of trust and admiration beyond what you'd expect. Okita, who is sick with tuberculosis that not even the water of life can cure - and the water of life would gradually drain his life anyway, mind you - finally states that maybe Hijikata wasn't so bad after all. It's then that Saito smiles and turns his back on him. "Souji, we should go on," is what he says, but he gets no response. When he turns back, only Okita's sword is there, causing Saito to drink the water of life and go on a rampage killing furies - using both swords to honor his fallen partner and feel him by his side once more.
Episode 18 of the anime starts badly with a flashback of Kondou being executed, follows with Harada's implied death from a wound he sustained in a battle against Koudou and tops it off with Okita's Heroic Sacrifice as he uses up his life force to defend Hijikata from an assassin squad... Hijikata gets wind of what he's doing and, still badly injured, limps painfully out of town towards the spot, but by the time he gets there the only thing left is a bunch of dead bodies and Okita's sword.
:Oh my God.