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Tear Jerker: JoJo's Bizarre Adventure
JoJo's Bizarre Adventure is famous for its Crazy Awesome-nesss and overall Badassery, however, this is a multi-generational epic of the conflict and tragedy brought upon by a traitorous adopted son's ambitions which have all had caused calamities either through direct or indirect influence that made the protagonists and their friends suffer for over a century.
The death of Jonathan's dog, Danny, is particularly crushing because the animal was the closest thing Jonathan had to a friend, and it's even sadder because of how easily it could have been prevented. The dog died only because Dio lost against Jonathan in a fair fight, and he got him killed in the cruellest way possible. To clarify note stuffing him inside the outside furnace and him being muffled; thus one of the servants wouldn't know that they were unknowingly burning Danny alive. Yikes! The first truly saddening moment in the series underscores just how much of a bastard Dio is.
At the beginning of the Genre Shift, George Joestar protects Jonathan from Dio's dagger, and then dies in his arms. This is after making a speech on how he was sorry he was so hard on him since his youth.
Bruford's tragic backstory, as well as his inevitable fate: Both he and Tarkus sacrificed themselves in order to save their master, Queen Mary, but Reality Ensues since Elizabeth, her political rival had already had her killed. With the revelation of their Senseless Sacrifice, it's little wonder why both her and especially, Tarkus lost faith in humanity and became easy for Dio to control.
The death of Will Zeppeli. He knew he was inevitably going to die the way he did, so he used it to Jonathan's advantage.
The death of Jonathan Joestar: he dies to save his wife, an infant of a woman killed by a zombie to which he had no connections to, and unborn child, on his honeymoon no less, taking Big Bad Dio down to the bottom of the sea with him. Made all the sadder by the smile on his face when he dies, directed at his wife, the readers, and Dio himself.
There's also the fact that in the end, even after all the damage Dio did, Jonathan was able to forgive him and call their relationship a "bizarre friendship". He even felt sorrow for when he thought he was dead after beating him finally. Talk about Too Good for This Sinful Earth.
What makes this scene even more tragic was that in the long run, his sacrifice was pointless. Thanks to being stuck under the sea for a hundred years Dio came back stronger, smarter, more Dangerously Genre Savvy, and even more ruthless than he was before. Hell, his revival started many tragedies because Jonathan tried to bring Dio down with him. And then his last words to his Wife are even more heart-wrenching:
Stroheim's Heroic Sacrifice through a suicide by hand-grenade to stop Santana from being unleashed upon humanity; one of the few times you will ever cry for any Nazi, let alone one as heroic as him. Heck, even Jojo himself was crying with respect for his bravery. Making it even more awesome when he comes back as a cyborg to briefly fight on par with Kars for a short time, and even brought back as a cast regular
Mark's death at the hands of Wamuu, another example of Too Good for This Sinful Earth; he was one of Caesar's only friends. In spite of being a Nazi with great enthusiasm to the cause, he had plans to marry to his girlfriend after the war. These plans are cut short when the Pillar Man walks and absorbs half of his body while not even bothering to notice, his last words were to die a painless death. Such a pointless Kick the Dog moment filled with Lack of Empathy fueled both Caesar and Joseph with intense vengeance...and campyposes.
The flashback regarding Caesar's backstory, after years of wanting to exact revenge on his father for leaving him he gets saved by him before he could be killed by the Pillar Men's trap. The wrenching part about it all? His father died without knowing he just saved his son.
Caesar's death. From the very realization he's dead Joseph and Lisa Lisa are clearly distraught and trying their best to maintain their composure as they continue on deeper in to the mansion, and then they find where Caesar died under the piece of debris. The moment they see it Lisa Lisa, who was up until now the calmest of the group, breaks down into tears along with Joseph who screams his name complete with highly emotional Manly Tears. Only silence answers them.
The Anime recreates both this scene and Caesar's backstory in the same episode. It's depicted fantastically and is every bit as tragic in the manga, especially on how they deliver it. "Il Mare Eterno Nella Mia Anima" sums up the tearful emotions of the scene so perfectly it hurts.
Elizabeth Joestar aka Lisa Lisa's backstory, involves her killing the zombie that killed her husband, George Joestar. Unfortunately, he had impersonated a highly ranked officer, which when found out by a hapless soldier, led to her to force to leave her son, Joseph in the care of her mother in law while she was on the run as a fugitive The kicker, the zombie was one of Dio's surviving members of his army, making the couple, another victim of Dio's ambition
Avdol's first death, trying to save Polnareff. It was actually a cover-up to hide from the enemy in order to heal up, but Polnareff's tears at the sight of what he thought was his death and trying to kill Hanged Man for insulting him is very tear swelling.
N'Doul's death, after being beaten by Jotaro, he uses his Stand to kill himself in order to not spill out any information on his allies, especially Dio. He then tells how his life had no value till Dio came into his life and acknowledged him. Jotaro buried his body in respect, wondering why would people like would follow Dio.
Avdol's second death, also trying to save Polnareff. It's so sudden that Polnareff feels immediate guilt and anger towards Vanilla Ice once he reveals he killed him.
Iggy's death. Especially since he died saving Polnareff, the guy he'd spent the entire series bickering with.
Polnareff after defeating Vanilla Ice, witnesses the spirit of his two friends floating away giving him their acknowledgement, driving the big man to tears.
Kakyoin's death. It makes it worse that you get to hear his final thoughts, and they're about his unseen parents, who have no idea where their son is and what's happened to him.
Joseph's "death", especially how he gives advice from beyond the grave to help Jotaro not be blindly angered by his death and how he enjoyed the adventure he had with him.
Diamond Is Unbreakable
Josuke having to accept that his stand can't bring his grandfather back to life.
Rohan coming to the realization that the Ghost Girl was once his baby sitter, killed by Kira prior gaining a Stand.
Shigechi's death. Made even more sad by his last Harvest giving Josuke a clue to the killer and then cutting to Reimi seeing his spirit ascending to the afterlife, screaming in pain. Made even worse when you remember how he even got into the mess leading up to his death; all he wanted was to eat his sandwich.
Hayato being forced into becoming a Tyke Bomb while Kira gloated on how helpless he was, makes you feel really sorry for a brat who put hidden cameras to check his mother without her knowledge.
Shinobu Kawajiri waiting for her husband to come home, not knowing he had been killed and replaced by Kira many days ago, who himself died recently. To make matters worse, she hated Kosaku, but adored Kira as Kosaku, not knowing she'd fallen in love with a character acted out by a serial killer.
The sudden deaths of Abbachio and Narancia, with the former recalling his failures as a failed cop who let his friend die due to his bribery and the latter wanting to return to his hometown
Bruno's death at the hands of Diavolo, who by his friend's Stand power, manages to survive while slowly breaking down to eventual death accumulating in his true and final death via Heroic Sacrifice in order to stop the mad mafia boss' ambitions by giving time for Giorno to gain the Requiem power
The end of part 5 where Giorno, despite being hardened for the series finally starts to tear up at the loss of his friends Buccarati, Narancia and Abbachio he fought alongside, until Buccarati's spirit talks to him and encourages him along with Narancia and Abbachio departing. He mans up and takes hold of his (and Buccairati's) dream for them.
Polneraff may have been switched into a turtle's body for the rest of his life, However, his recall to his adventures and losses in Part 3 is very tearjerking for what was thought to be his last thoughts at the time.
Weather Report's death at Pucci's hands, something that would've ended the conflict; had Jolyne not arrived at the wrong time to give the Big Bad a chance to kill the former. Even more emotional baggage for Jolyne to deal with.
"Look at me Jolyne. This is my spirit. This is my intellect. I was alive."
Hermes, Anasui and Jotaro's deaths at the hands of Pucci's new stand.
The Bittersweet Ending itself. Yes, the Big Bad is dead, and Emporio survived...but he's the only one left who can remember their friendship. Making matters worse, all the suffering the Joestar Family endured in the 129 years since the adoption of Dio Brando has now literally all been for less-than-nothing. The only thing that keeps this from being a downer ending is that Emporio may be able to befriend the now well-adjusted Jolyne and friends once more.
Steel Ball Run
Johnny's past regarding the death of his older brother Nicolas; he never stopped blaming himself for it where its most likely not even his fault, and how his father blatantly favored Nicolas over Johnny, years after his brother's death. The latter is made all the more heartbreaking when its clear that Johnny desperately wanted his Father's affection.
"Ahh...God, you took the wrong son."
Gyro's death. We are treated to a close up on Johnny's visibly heartbroken expression, as well as a flashback to everything that had happened before. Johnny doesn't even scream out his name; everything happened so fast and he was so dumbfounded that he couldn't do anything but watch, teary eyed and desperate.
After killing Funny Valentine, he sees his ghost and the latter gives his farewells. Followed by several page spread of their memories of building a strong bond.
The fate of the unnamed woman in Ojirou bathroom. Unable to move for fear that she may get cut by Ojirou booby trapped house and his stand could take effect.
The continuation of Johnny's life didn't end with a Happy Ending as it turns out he died to protect his wife from a disease. To make Johnny's life worse, when he tried to heal his wife, Rina, from her paper-folding disease with the Holy Corpse parts, he accidentally transfered the disease to his son, then to himself. The only way was to make sure it didn't spread any further to was kill himself. Ouch.
Josuke tears up a little when he sees a happy family playing around and is reminded that absolutely no one came to look for him when he went missing and lost his memory. The revelation that he's not even a true person due to being an amalgamation of Kira and someone else only makes it worse.
Similarly, Josuke desperately hugging Yasuho after the two were separated, because she's his anchor in 'a world of strangers'.
Yoshikage Kira's fate in the one-shot story Dead Man's Questions, especially for a man who just wanted to live a quiet, peaceful life. He gets to live the same struggles as the rest of the living beings, with the addition of not knowing who he was while being alive. There's no "Rest In Peace" for him.
The ending for Kakyoin in the Capcom fighter: He manages to defeat Dio, but is mortally wounded by him in the process. He tells Jotaro and Joesph that he's fine on the flight back to Japan, but passes away shortly thereafter, telling Avdol and Iggi that he would be joining them soon. Jotaro's reaction to Kakyoin's death in the last moments of the ending makes it all the sadder...