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Tear Jerker: D.Gray-Man
"I'm a crybaby... am I right?"
There's no denying that D.Gray-Man is a series that loves to render its audience inconsolable.
The Ghost of Martel arc is definitely one of the saddest moments in the series. It doesn't help that it's got such a haunting song in it as well...
"May I sing a song for you...?"
"Are you going to sleep? I will sing you a lullaby then."
Bonus points for the song being Verse 18 of Mozart's Requiem Mass in D minor.
Allen's flashback from the Jean and Leo arc.. His cries for Mana to come back to life were so heartwrenching to hear.
Then there's the Fallen One arc. After Allen tries so desperately to save Suman, and then finds out his efforts were all for naught, since he'd already lost his soul, we get a flash to his daughter lying in a hospital bed, saying she had a dream where her father was waving goodbye.
Lenalee asking Lavi if she is still in this world after nearly dying. It's so touching, that later Road uses it to Mind Rape Lavi.
Seeing Lenalee completely break down mentally after Suman turns into a Fallen One followed shortly by the presumed brutal death of Allen at the hands of Tyki. The worst part is she gets to see the painful process through Timcanpy. And when the Asia Branch recovers him to their headquarters, she isnīt even allowed to see him.
Lavi's whole internal battle against Road (though it's really more against himself thanks to her powers of Mind Rape) involves him revealing that he's not supposed to care about the people at the Order but now sees them as his friends. He's also being forced to kill illusions of them, until his "heart" dies and he becomes emotionless. This causes him to try and kill Allen (who can't figure out how to save him without killing him) while Lenalee helplessly screams for him to stop. When Allen is about to be killed, Lenalee realizes that Lavi was using his Flame Seal to melt the candles Road was using to threaten her and Chaozii. It is shown inside Road's dreamworld that Lavi stabbed himself to keep from being completely controlled, and he then uses the Flame Seal on himself in the real world. Then, in the dream world, he stabs the illusion of Allen because he'd figured out it was actually Road in disguise, and then talks to two past versions of himself, who question him and ask him why he's different from them, to which he replies that they're the same person. All of this happens while Allen is trying to save Lavi from the Flame Seal and yelling his name. When the past Lavi (which is a small child who first became a bookman) hears Allen's voice, he realizes that what Lavi was saying was true and escapes from the dreamworld. This turns it into a Crowning Momentof Heartwarming. Yes, the whole thing is very confusing if you haven't actually seen it.
There's the end of the journey to Japan. All the exorcists assemble on deck with three of the crewmembers, Anita and Mahoja, the only members of the crew not to have been fatally struck during the many battles on the trip. All the the doomed crewmembers call out to the exorcists to win, and all the survivors climb into a lifeboat. Then, Lenalee reaches out to help Anita on, and Anita strokes Lenalee's hair and tells her to grow it out again. At that point they realise that Anita and Mahoja are doomed as well. The look on Lenalee's face as she realises this is heartbreaking. It's also heartbreaking for Miranda as well- her Innocence was the only thing holding the ship together and keeping the crew alive. The way she cries when she admits she can can no longer keep it active takes from the audience as well.
During the battle with the Level Four, when Lenalee synchs with her evolved Innocence. It turns to a pool of liquid in her hands, and as she is about to drink it, her brother Komui runs to her, almost on the verge of tears. She looks at him, and then gives him the most heartbreaking smile ever, and says "I'm off then, Brother" before drinking and synching with the Innocence. Made more poignant since if she doesn't synchronize with the innocence, it will kill her.
Lenalee:"So please, for now, say 'take care'. Because I want to smile and say 'I'm home' again."
The death of Tup. He had been transformed into a Skull and there is nothing his friends could do but hold him and watch as he will turn to dust and die. After being transformed into a Skull, Tup had no memories of his past life and wasn't responding to his friends' cries. Not until a few tears from a sobbing Johnny landed on his face. He then remembered how he was exhausted from overtime and wanted to sleep, so much that if he could, he didn't feel like waking up again. Then he told Johnny, with tears in his eyes, showing that he was back to normal, even if it was only briefly.
"If I could live, I wouldn't care if I had overtime forever ..."
What made it even worse was the reactions of all his friends as they watched him die. Especially Allen, who wasn't there to see Tup's final moments but knew that he had died.
Heck, even Kanda had what could be called a sad look on his face, and he usually acts indifferent towards things like that.
The scene where Tyki gets stabbed and Road panics a bit and goes to help him, after which he smiles at her and tells her it's okay. He then gets stabbed AGAIN and falls unconscious. Later, Road tells Lero to make sure he doesn't get burned in a fight... and later-later, his Noah awakens fully and he spends several minutes screaming in agony before he transforms into Joyd's true form.
Then, in later chapters, we see Road and Tyki in a room full of broken glass, with Road bleeding, and Tyki sitting there shaking, holding his head, covered in scars and telling Road that it hurts.
God do the Noah get a lot of unexpected b'awww moments. The part where it's Skinn's farewell party, and they're all being made to cry due to Noah's sadness and pain. Jeeesus, this family is insane.
The Krory and Eliade arc. Krory is an exorcist and Eliade is an Akuma, so despite them being in love, he has to kill her, and during their fight she tells him that she was just using him. Then, when she thinks she's killed him, she turns back into her human form and walks towards him to say goodbye, only for him to suck out her blood from her neck and restore his health while crying, and she tells him that she loved him before turning into dust.
Pretty much any scene accompanied by this track from the OST.
The story from the very first chapters (must've been the second) that this track was named after deserves a mention as well. Those poor boys. Poor Jean and poor, poor, miserable Leo. Seems like it's a general rule in D.Gray-man that there must be tears in the end.
Pictured above: In episode 11, Miranda's inner thoughts right before she fully releases her Innocence completely brokemy heart.
Miranda: "As far as I remember, nobody ever thanked me. Everyone turned their backs on me. No matter what I do, I do it wrong. I can't help anybody. I can only be left behind, even if it hurts. But still. Even when I can't do anything well, I'll try anyway. Even though I decide to not try anymore, I regret it, and I attempt it again... After all, I can't do anything right. it's better if I don't try at all. I'm an idiot, am I right...?"
And there's the scene in the manga (the anime didn't get far enough) where abusiveParental SubstituteTrickster Mentor General Cross Marian shows that he's not acompletely heartless bastard when he has to tell Allen that he's the host for the Fourteenth Noah, and will eventually have his personality subsumed and be forced to fight his friends. He hugs him, apologizes, and rails against the Fourteenth for choosing someone with friends and a future like Allen. After Allen leaves, he says he can't make fun of General Tiedoll for being soft-hearted about his students anymore...
The recent arc involving Kanda's and Alma's past has been really sad for the most part. Then chapter 193 came along in which Alma is driven to a massive killing spree, only to stop when he sees his best friend show up. Then after greeting him and cheerfully telling him he is going to kill him he attacks Kanda. Sadly, the fight doesn't go very long before Kanda is forced to strike down his only friend. After reading this any sympathy I had for the Black Order has been completely erased. I know they are trying to win a war, but for gods sakes they ended up forcing a CHILD to go on a rampage and fight his only friend AND forced said only friend (ALSO A CHILD!) to kill him in self defence.
Keep in mind that this incident is what broke any cuteness Kanda had to begin with, turning him into the Jerkass we know today.
Detailing on the aftermatch of the example above, Volume 20 came out with the three-pages-long extra chapter 193.5 - Have a handkerchief or two at hand... It's made 10 times worse by the simple fact that the other extra material in that volume are expanded bios on the flashback chapters
From the anime we have a flashback to the accident that resulted in Mana's death. What makes it worse is you already know what happens after that and how Allen got his scar...
Chapter 198 when you place the face of Alma's predecessor that Allen sees Kanda and Alma's attempts to kill each other and Alma's earlier attempt at a double-suicide all the sadder.
Tokusa tearfully asking Madarao to absorb him after he loses both arms and can't fight, rendering him useless. By having Madarao - the most likely candidate to become a new womb - absorb him, he hopes to live on and still contribute to the war effort. Why? "Because we too would like to save this world".
Just the entire concept of the Akuma can teeter between nightmarish and Tear Jerker depending on how you look at it. You lose someone you love, someone you cared for so deeply that fat demons in trenchcoats wearing funny hats and ridiculous grins can feel it and approach you with the offer to bring them back. You agree to do so, and you'll find out that you brought back your loved one in the form of a metallic skeleton or some other mutilated variation thereof that proceeds to kill you because they have no other choice but to do so unless you kill them first, leaving either you dead and the resulting loved one ripping the skin off your body to wear as their own and take your identity from then on or for you to kill them (somehow), causing you to lose them all over again. And then there's the akuma itself. They were brought back to life against their will, only to be forced to murder the very person who brought them back to life, usually the same person whom they loved dearly. Then they would take over their loved one's body and resume their identity, usually portraying them as being of little emotion or ones many others would mistake as complete bliss, incredible obsession or extreme depression (or something else entirely...). Inside, they're a tortured soul, forced to kill many while trapped in a body they can't always fully control, serving their purpose only as a bio-weapon of some sort whose only salvation is being killed by another. Oh, but not just any person! If you aren't killed by an exorcist, or their weapons, such as you, say, managed to kill yourself, your soul will be lost forever with no hope of being saved.
The part where Allen had tried to exorcise a collection of akumas masquerading as a happy family, only to be left crying in grief when one of the akuma blew themselves up before he could reap them, losing that soul.
Kanda and Alma have so many moments but chapter 200 topped it all. Thought you'd never see Kanda hold someone and cling? How about Kanda crying and smiling while holding his dying beloved ? Doesn't help that the goddamned lotuses turned up again, possibly hinting that he died as well.
Chapter 202 gave us an indication about that last line. Everyone in the story is assuming Kanda has died with Alma. You may bawl your eyes out now.
When the smoke clears and we see Kanda's messed up body, the whole of the end of the Alma-Kanda arc... both heartwarming and tearjerking.
Though at the end of chapter 207, Kanda has returned to the Order. A bit dirty, but his very Kanda-like smirk is enough to warm any fangirl's heart.
Tewaku stumbling around the battlefield, still horribly mutated and crying for her brother and companions, delivers this line just before Millennium Earl uses the Ark on her.
The 14th's melody is especially beautiful and sad 
The end flashback of the Earl of all people is this as it implies that the 14th Nea is responsible for the former's insanity
Chapter 193.5 where it shows For carrying Edgar's dead body, and setting it up next to his coworker. She's talking to them as she's carrying them, and ends it by berating them for ordering her not to protect them. "My god, what the hell were you thinking? Turning down the protection of a guardian angel......you crazy idiots...."
This troper has only seen one episode of the animenote and a few volumes of the comics and the song "Musician (Tsunaida te ni kisu wo)" makes her very sad. Especially as it's sung by Allen's voice actress and could be seen as his perspective.