Unmarked Spoilers Ahead!
"I am sick of it...Having people up and die on me.. Im so sick of it... YOU HEAR ME?!"
- Advol's first "death" is terribly sad even if it wasn't permanent. First, Polnareff lashes out at him, pushing all of his Berserk Buttons before storming off, their budding friendship in tatters. Then Polnareff lets Hol Horse goad him into a fight he can't win — because J. Geil's Hanged Man was lurking out of sight, waiting to ambush him — leaving Advol no choice but to defend Polnareff with his life. He's promptly stabbed in the back and shot in the face just a few feet from Polnareff and Kakyoin, who was just a second too late to save him. Kakyoin is visibly devastated and even clings to his body, begging him to wake up; only for Polnareff to turn his back on them and launch into an angry tirade seemingly insulting Advol's sacrifice. Just as Kakyoin grows furious on Advol's behalf, Polnareff peers over his shoulder, revealing that he's outright bawling.
- Hol Horse and especially J. Geil tormenting Polnareff afterward by gleefully reminding him that Advol's death was his fault; and in the latter's case, how horribly his defenceless little sister died. The story arc doesn't exactly show Polnareff in the best light before his character development, but you can't help but feel bad for him when the enemy toys with his emotions in such a cruel way.
- Between Kakyoin actually shedding a few tears, Joseph ruefully calling Advol his old friend while kneeling beside his body, and even Jotaro clenching his bloody scarf in helpless fury, it's clear Polnareff wasn't the only one who took Advol's "death" hard. It's an excellent indication of how close the crusaders have grown.
- Enya's death is surprisingly sad, despite being a horrible person who was a very bad judge on her arguably worse son's character. DIO had an assassin kill her off on the off chance she'd reveal his power despite all of her loyalty to him and having no intentions of revealing it anyhow. Just leaves a bad taste in the heroes' mouths and underscores how little DIO cares about his underlings.
- 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. Before he dies, he acknowledges Jotaro's strength, and explains to Jotaro how he lived a lonely and miserable life, due to his blindness and Stand powers isolating him and forcing him to survive on petty crime, until he met DIO; who acknowledged him for he was, and gave him purpose and value as a person. Jotaro eulogises his fallen foe and buries N'Doul's body respectfully — marking the spot with his jewelled cane — sadly wondering to himself why people like him turn out the way they do.
- On encountering Cameo, Polnareff is offered three wishes. After testing his first wish by asking wealth (which he is promptly given), Polnareff debates what his second and third wishes should be. At first he's torn between either his childhood dream of being a comic/manga artist or true love, but then he thinks of what he truly wants. He wishes for his sister, Cherie, to be brought back to life. And when he sees her apparently returned, and hears her speak, the look on his face is just heartbreaking. Polnareff is crying tears of pure joy, with the most genuinely happy look we've seen on his face in the entire anime. We're also treated glimpses of Polnareff and Cherie's childhood together, and you can see how much he really loved her. Turned into a combo of Tear Jerker and Nightmare Fuel when Cameo twists Polnareff's wish by turning Cherie into essentially a flesh-eating zombie that tries to kill him. And then to twist the knife even further, Cameo brings a fake Avdol back to life as well, who begins to tear into Polnareff psychologically. The poor guy can't catch any breaks.
- Polnareff and Joseph backing away from Kakyoin in fear (while Jotaro just watches it happen), whispering about him behind his back, and even considering abandoning him after Mannish Boy manipulates them into believing he's insane. These are the only friends Kakyoin's had. Not to mention Death 13 is constantly torturing him in his sleep, leaving him exhausted and mentally unwell.
- During the fight with Alessi, a random Egyptian woman takes Polnareff (at the time a seven-year-old) in and tries to help him. She gets deaged to a fetus by Alessi's Stand, only surviving because Jotaro and Polnareff beat the hell out of Alessi, undoing his power. When she comes to, she finds Polnareff's lost earring (he left it in the bath when Alessi tried to drown him) and runs out after the duo, asking if they've seen a young boy. Polnareff, not wanting to get an innocent woman caught up in their trouble, denies any knowledge. Now here's where the tear jerker comes in: in doing this, he abandons the earring, the only thing he had left of his sister. And as they walk away, he orders Jotaro not to say a word. Polnareff's various tribulations are played for laughs a lot, but this is a rather somber moment. Even more so if you know the usual kind of personality Polnareff has.
- When Suzi goes to visit her daughter Holly, it's clear that she is in failing health. Even still, Holly smiles warmly for her mother. Even with the grim specter of death looming over her, she never loses her positive outlook.
- Avdol's real 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 burning Vanilla Ice alive in sunlight for killing Avdol and Iggy, witnesses the spirits of his two friends and floating away giving him their acknowledgement, driving the big man to tears. The anime version drives the viewers to tears with some of the most heart-rending music played over the scene where their souls ascend to the afterlife, which itself has some of the best animation in the series.
- Polnareff tells himself afterward he doesn't have time to wallow in sadness, and that he needs to get to DIO despite everything that just happened. He then breaks down crying regardless.
Polnareff: I just realized how much I liked him. It always happens this way. I only understand after they're gone.
- The way he screams their names afterward, in both in the original and dub, is utterly heart-wrenching.
Polnareff: Avdol... (voice cracks) ...IGGY!
: It was only for a little while, but you should thank Avdol for extending your life. At that time, if he hadn't pushed you away, you would have been swallowed by the sub-dimension together.
He could have survived if he'd tried to escape alone. What an Idiot!
Polnareff: (wounded and lying on the ground) "Idiot", you say...?!
Polnareff: (trying to get up) Y-you...!
Vanilla Ice: You can still move? But, this is the end. Die as you regret your own stupidity.
- As Kakyoin vows to uncover the secret of DIO's Stand, we get a flashback to his youth — he was estranged from other kids his age, and even his own parents. It wasn't that anyone didn't try to reach out to him; rather, he never felt he could truly be understood by anyone because no one else could see his Stand, Hierophant Green. It wasn't until he met Jotaro and the others in the present day that he ever truly felt a bond with anyone.
Kakyoin: Yesterday, I knew that my reality was different from everyone else. Loneliness. Instead of trying to understand others, I had decided to give up until that day. The slight tingling of Emerald. I was wondering why I was still living.
- 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.
: I wonder if they got the letter I sent them... oh well, they probably didn't have time to read it anyway...
- The anime takes it a step further — after using his Stand in a last-ditch effort to tip off the others about the specific ability of DIO's Stand, Kakyoin's final thoughts are heard over haunting, sorrowful music as the color slowly bleeds out of the scene, reflecting his impending death:
Kakyoin: (in thought) It's a... message. It's the best I can do... Mr. Joestar
please understand. Please, figure it out...
- As a lot of fans have pointed out the saddest part about Kakyoin's death is the fact that the days he spent traveling with the protagonists were the best times in his life. Just as Kakyoin had finally found people he could truly call friends and reached the high point in his life, it was all cut short by DIO.
- Once again, Joseph Joestar has to watch a brilliant, brave young man die as he is unable to do anything to stop it. The trauma of Caesar Zeppeli's death follows him even into his old age, as shown in this splice of Old and Young Joseph◊ — the exact same expression of wracked grief, separated by decades.
- 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 Tear Jerker that such a kind and noble hero was so thoroughly desecrated after death.
- The ending for the second half of the anime. After the awesomeness of Yes's "Roundabout" for parts 1 and 2, and the jaunty "Walk Like an Egyptian" by The Bangles for the first half of part 3, we have the non-vocal and melancholy "Last Train Home" by Pat Metheny Group. The credits itself are mostly still frames, one includes a depressed Joseph holding three train tickets and the other shows Jotaro, Polnareff, and Joseph on one side of a bridge, while Avdol, Iggy, and Kakyoin are on the other side. The last shot of the ending animation is of the group photo the heroes took shortly after meeting Iggy, which becomes all the sadder when you realize that by the time the story ends, half of these brave heroes will die.