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Part 1 (Phantom Blood)
- Jonathan Joestar's death. He dies saving his wife and unborn child, on his honeymoon no less, taking Big Bad Dio Brando 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.
- Sir George Joestar's death.
"Don't look so sad, JoJo... Where better to die...than in the arms... of my... son?"
- Buford's tragic backstory and his inevitable fate.
- 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.
Part 2 (Battle Tendency)
- Caesar Zeppeli's death. Lisa Lisa and Joseph try their hardest not to cry, trying to stay strong... but then they see his body and it becomes too much to bear.
- Joseph's reaction does not help at all.
- Wamuu's death.
- The death of Mark the Nazi... at least until Joseph and Caesar react by dramatically posing in front of the Pillar Men.
Part 3 (Stardust Crusaders)
- Avdol dying after saving Polnareff from Hol Horse. Subverted when it's later revealed that he actually survived.
- Iggy's death. Especially since he died saving Polnareff, the guy he'd spent the entire series bickering with.
- 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.
- Polnareff, after defeating Vanilla Ice, sees the spirit of Iggy and Avdol floating away and giving him their acknowledgement, driving the big man to tears.
- The fact that DIO survived by tearing off Jonathan's head and attaching his own head to his body. Even after everything Jonathan went through, DIO still got exactly what he wanted, and it's a real shame to see such a kind and noble hero's legacy being so thoroughly desecrated after his death.
Part 4 (Diamond is Unbreakable)
Part 5 (Golden Wind)
- The end of Part 5 where Giorno, despite being hardened for the series, finally starts to tear up at the loss of his friends he fought alongside, until Buccarati's spirit talks to him and encourages him, along with Narancia and Abbacchio, before departing for the afterlife. He mans up and takes hold of his (and Buccairati's) dream for them.
Part 6 (Stone Ocean)
- 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.
- Jotaro's death. Even worse, the last thing he saw before Pucci sliced him in half was Jolyne getting stabbed by Made in Heaven's knives.
- Jolyne's death. She smiles at Emporio before standing up to Pucci one last time as he closes in. Then a page and a half later, you see her getting ripped apart like tissue paper by Made in Heaven as Emporio breaks down in tears. All that remains are Stone Free's sunglasses, which quickly disintegrate under accelerated time as a colony of butterflies flutter off.
- FF's death. Made even worse by the fact that she was the only one of Jolyne's allies who wasn't reincarnated after the universal reset.
"Look at me, Jolyne. This is my spirit. This is my intellect. I was alive."
- The ending. Yes, the Big Bad is dead and Emporio survived... but he's now stuck in an alternate timeline where none of his former companions have any idea who he is. The only upside is that he might be able to make friends with Jolyne's more well-adjusted counterpart.
- In a meta sense, the fact that this part is the last time the original continuity was ever visited in the manga. For those who have read all the way from Phantom Blood, it can be very saddening to see the story that started with Jonathan Joestar and Dio Brando come to a close, especially after all the time spent reading each part of the story. Though for long-time fans, it may hit them even harder seeing as how the earliest fans have been keeping up with the franchise since 1987 and, with Stone Ocean ending in 2003, that meant 16 years of reading JoJo. While Steel Ball Run is considered one of the best parts in the franchise, it's still tough for a lot of people to fully realize that Stone Ocean was the last we'd ever see of all the classic characters and locations.
Part 7 (Steel Ball Run)
- Gyro Zeppeli's death. Even in the new timeline, the Zeppelis just can't catch a break.
- Diego Brando's death. At least he died happy, believing that he'd killed Valentine.
Part 8 (JoJolion)
- The end of Johnny Joestar's life, where the Joestar Curse claims another victim.
- The death of the new timeline's Yoshikage Kira - and in a Heroic Sacrifice, no less.
- Yasuho was nearly Driven to Suicide at age 13 thanks to a Rock Animal tormenting her non-stop.
Eyes of Heaven
- Jolyne screaming "It's all your fault I'm like this! YOUR FAULT!" at DiU!Jotaro. Ermes also asks SC!Jotaro to be more attentive once his daughter is born.
- Thankfully, the post-credits scene reveals that Jotaro took Ermes' advice to heart, as we see him bringing a young Jolyne to Morioh in the hopes that she'll grow up to become a better person.
- The sheer shock and disappointment in Jo2uke's voice after he meets Yoshikage Kira and is told that he's a serial killer.
Jo2uke: "Wait! Are you really Yoshikage Kira?"
Kira: "Indeed... but not the one you're looking for."
- Old Joseph stepping in to prevent an argument between his younger self and Caesar (specifically, the one that led to Caesar running off and getting himself killed by the Pillar Men). He lectures the younger Joseph on not being so cocky and thinking he knows everything, while he warns Caesar that, while his desire to avenge his grandfather's death is noble, he shouldn't forget about those who care about him and are still alive. Even after 50 years, it's clear that Joseph still sees Caesar's death as his biggest regret.
- Heaven Ascension DIO killing Jolyne in front of Jotaro.