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Tear Jerker: Ultimate Spider-Man
Ultimate Spider-Man gets a few, but one of the most poignant is after J. Jonah Jameson fires Peter. After a run-in with the Kingpin's goons (during which Spider-Man saved him) and a fierce phone call from Aunt May, Jameson walks to Peter's house late at night and waits for him to return. He sits with Peter on the stoop and gives a heartfelt explanation of why he snapped and fired Peter when he asked what was so wrong with Spider-Man. Jameson, in a rare sympathetic moment, tells Peter that a few years ago his son, who meant the world to him, was killed in a NASA shuttle accident. The agency sealed everything off as classified, and Jameson didn't even get a body to bury. He says that his son was a hero, that men like that are real heroes, and that people like Spider-man just cause chaos. Even though the reader (and obviously Peter) disagree with him on that issue, it is such a heartwarming yet simultaneously heart-wrenching moment of weakness and grief from the grouchy old man that no one can hold it against him, topped off by Jameson rehiring Peter and telling him that he'll assign him to Ben Urich so that he can learn what reporting is really about.
And Jameson's realization that he was wrong about Spider-Man, something that sadly could never happen in the mainstream series thanks to Status Quo Is God.
In Ultimate Spider-Man when Spider-Man dies. Crosses into Fridge Horror if you believe that both the Ultimate Peter Parker and the Mainstream Peter Parker share many of the same traits.
All of Ultimate Fallout. Everyone's reaction to Peter's death is emotional. Captain America QUITS over it, Nick Fury also feels responsible, and the city of New York mourns, to the point that thousands pay their respects at the funeral.
Mary Jane: "What are you going to do to me...?"
Nick Fury: "I loved him." Mary Jane looks at him in shock. "I met him when he was just a baby. His parents were working on a project for us."
Mary Jane: "You knew his parents?"
Nick Fury: "Yes."
Mary Jane: "I-I didn't know that."
Nick Fury: "When his parents died, I wondered if I there was any way I'd be able to do right by them. And then I was so excited when he had the accident that gave him his powers. Now I could do something. I was grooming him, you know. I was so sure he would grow up to be the man his father wanted him to be and so much more. This brave, one-of-a-kind genius little boy. I should have taught him more, I should have slowed down the world so a boy like him could become the man he was supposed to become."
Mary Jane: "I didn't know you knew his parents." Nick Fury pauses and she continues. "Okay I won't-I'm not going to send out anything I wrote. I didn't know.'
Nick Fury: "I understand you're looking for someone to blame for this...my point is...you blame me...and I came to tell you...you're absolutely right.*tear goes down his cheek*"
The first Fallout issue is this for pretty much every page.
When Aunt May invites Gwen to live with her and Peter, and Gwen just throws herself into her arms and starts to bawl.
The lottery. Every single kid there is gifted, but whether they're going to get a decent chance depends on whether they're lucky enough to be picked from a lottery.
Miles mother dying in his arms is heart wrenching. Made worse the next day when he wakes up to realize the nightmare was real.
Spider-Men features the exchange where 616 Spider-Man meets Ultimate Aunt May and Gwen Stacy. They're naturally asking lots of questions about their counterparts, and when Gwen asks Peter what she's like in his world, he hesitates for a moment, then just smiles and tells her that she's awesome.